Transformers: The Atlantis Factor
by Wraith Queen 500
Summary: John Sheppard loves all those he calls family but somtimes they irritate him to no end. His adopted nephew Sam Witwiky is no exeption to this fact and the giant alien robots really aren't helping.
1. Chapter 1

Disclamor: I own nothing.

_**Flash Back**_

_t__hought_

Telepathic Talk

I also thank Botosphere for the use of their idea in the fanfiction Kinship. The idea belongs to them. I will also make some small refrences to their story and would recomend it to anyone. the story also has a segual called 'The Ties that Bind'.

* * *

Chapter One:

"Come on Sammie, he'll be here soon."

"It's just my Uncle mom," whined Sam.

"Who you haven't seen in six years, and have you forgotten? He's going to meet Mikaela," said Judy.

"I think it will be nice to meat your Uncle…" said Mikaela, fishing for a name.

"John, Uncle John," replied Sam, "we're mot actually related but he's still my uncle. Don't forget to keep that toy car quiet."

"Wheelie's a good boy," smirked Mikaela, "unlike some people."

Before Sam could retort, a knock sounded on the door.

"He's here," squealed Judy while Ron went to answer the door.

Truth be told, Sam really was looking forward to this, two whole weeks of normal. He had made both Lennox and Optimus swear to leave him be for the time his Uncle was over.

"_**Look, two week is all I'm asking for," protested Sam, "I need some normal and my Uncle, who I haven't seen in years, is coming over for the holiday."**_

"_**Sam I know you want normal, but I don't think the Decepticons care," argued Lennox.**_

"_**He's right Cube-brain," agreed Simmons.**_

"_**If Megatron believes you are unprotected, he will attempt to capture you… again," intoned Optimus worriedly.**_

"_**I'll have Bee with me, and if something happens I'll call, right away," promised Sam.**_

"_**He's safe with me,' sang over Bumblebee's radio.**_

"_**I can't believe I'm going to say this, but alright, however, you call us at the FIRST sigh of trouble," said Lennox.**_

"_**Thanks Guys," grinned Sam.**_

Since the incident with the Fallen eight months ago and becoming the offical ambassador for the Autobots as well as becoming the human Prime he had be under constant guard. Usually it was by Bee or the twins who still freaked his roommate, Leo, out. Simmons was allowed to work with NEST as a consultant, which made him pleased as punch. The cube still filled his head with bit of stuff every once and a while, nothing major though. He spent most of his time in class or at the NEST base consulting with govnment officals, which he finally got Mikaela and Leo clearance for, under some for of guard. (Lukily Optimus and Lennox got the guards to leave him alone when he was with one of the Autobots) He loved it because he could help the Autobots, his secertay was a nice guy and he had the spark-bond with Optimus but it was putting his normal life in a deep dark hole he may never get out of. He ginned when his dad fallowed by his Uncle came around the corner.

"Hey, kid," grinned John, hugging him.

"John, may I introduce Mikaela Banes," introduced Ron,' Mikaela, this is Sam's Uncle John Sheppard."

"Please to meet cha," smiled John, raising a hand.

"Right back at you," said Mikaela, who accepted the offering.

They all went to the living room where Sam and Mikaela sat on one couch and while Judy, Ron and John sat on the other.

"So, How have you been?" asked John.

"I've gotten into Collage, got a girlfriend, you know the normal boring stuff," said Sam. _I also discovered an Alien race and now one lives in my dad's garage. _"What about you?"

"Me? Well let see, I've been promoted Lt. Colonel, still fly planes _and puddlejumpers, _and do that generally boring and somehow necessary mound of stuff they call paperwork," grinned John. _I also fight wraith, live in another galaxy, and try not to die on a daily bases._

"You're in the Military?" asked Mikaela.

"Yeah, I'm in the Air force," said John.

"Hey Sam, Why don't you and Mikaela show John around Town," suggested Ron.

"Yeah, that's a great idea. I haven't se…" said john before he suddenly tripped.

It took all of Sam restraint to not yell at the ex-Deceptican that had suddenly been under John's feet. Sam guessed that Bee asked him to snoop since bee himself couldn't.

"When the hell did that get there?" exclaimed John as he stared that the toy car by his feet.

"I'm so sorry, I must have left it there earlier," Said Mikaela, who quickly crossed the room and picked it up, "are you ok?"

"I'm fine," smiled John skeptically.

He let it go, it wasn't her fault. But one thing is fore sure it you did not fight wraith in vast amounts of forests and not learn to watch you surrounding very carefully and one thing he knew was that toy card had not been there before. Once Mikaela retuned, she and Sam fallowed John throw the door. She discovered that while she was scolding Wheelie, John had learned about Sam's Car.

"Reminds me of the first car I had," said John

"It does?" asked Sam.

"Yeah, except mine was a dark blue Camero, not yellow with racing stripes."

The Three of them got into the car with Sam at the wheel, John in the passengers seat and Mikaela in the back.

"Still the Same old place?" grinned John.

Yep, still hasn't changed much," said Sam.

"They did add a new mall though," pointed out Mikaela.

"True," agreed Sam.

"Have you been?" asked John.

"No" they replied.

"Want to?" asked John

"Sure, why not."

About Ten minutes later they were all inside the huge building. Sam paled when they passed the food court but luckily john and Mikaela were not paying attention.

"Hey, I'll catch up in a minute. I need to use the restroom," said Sam.

"Alright Kid, We'll be over there," pointed John.

Once Sam got far enough away he dubbed back to the far side of the food court.

"Two week, you couldn't even give me that could you?" demanded Sam.

"Look Sam, Optimus detected increased Deceptican activity in this area, we're only here as a precaution," said Lennox who had jumped when Sam was suddenly behind him.

"Then why's he here?" asked Sam.

"Nice way to greet your roommate, Bro," replied Leo.

"Simmons said he needed training and roped us into dragging him along," grunted Epps.

"He is an armature who needs to learn," said Simmons.

"Who else is here?" growled Sam, growing impatient.

"Ironhide and the Twins," answered Lennox.

"Fine, just leave me alone," sighed Sam, walking off without giving Lennox time to answer.

"Touché much," grunted Leo.

"You can hardly blame him," sighed Lennox.

"True," agreed Epps.

Seeing Lennox and his team had not helped his day by any means. He met up with John and Mikaela who seemed to get along great. When they asked if there was any place he wanted to go Sam said no. Mom would be done with dinner soon and it was getting late.

On the way home Sam saw a Red Lamborghini, he paid it no attention. He knew what it was, and that it was fallowing him. One of the gifts the cube had given him allowed him to know if it was a Decepticon or an ordinary car. The people at NEST had puzzled over it, they couldn't figure out how he did it, he just did. It made no move to attack and Sam wasn't going to call Lennox. The Major had already broken that deal. Unfortunately for Sam, John also saw the car and thanks to his keen eyes he could tell the cars driver was not real.

* * *

Please Leave a review, prettly please?


	2. Chapter 2

I own nothing, though i would love to own stargate cause then I'd be rich.

* * *

Chapter Two:

"He wasn't happy to say the least," said Lennox.

"We did promise to leave him alone," pointed out Ironhide.

"I know, quit pointing it out," shouted Lennox kicking the dash.

"Hey!" cried Ironhide.

Lennox felt lucky that he was so close to the weapon's specialist, because anyone else would have been a smoldering mess on the sidewalk for daring to kick Ironhide. Of course Optimus wouldn't be happy at all and Ironhide would say it was a lucky accident.

"You guys having any luck?" asked Lennox

"Na, just some lame-ass Deceptican punks," came Mudflap's reply over the radio.

"According to Big man there are Five Decepticons including Barricade and Breakdown," said Epps.

"Yeah, and that's five to many," whined Leo over the radio.

"Remind me again why we brought him along?" asked Lennox. Epps just shrugged. "Alright let me know if anything changes."

* * *

To say dinner was normal would be too generous but to say it was awkward was too cruel. Sam had kept silent about seeing Lennox at the mall. Trying to not talk about aliens when everyone else but one person knew about them was hard. When his Mom had heard that Uncle John was in town she invited him over immediately. She had made them all swear not to talk or even think about the Autobot. Sam did have a very interesting conversation about Astronomy with his Uncle, but then he started to think about Lennox and the Autobots.

He loved his family, he really did. The problem was he didn't do heartwarming, he had told Teyla as much. He thought it funny that his family was a bunch of people he wasn't physically related to, but they were still good people. It was easier on Atlantis; he didn't have to hide anything there. He had known Judy since he was nine; he had been there when she married Ron and when Sam was born too. The kid called him uncle but he was more like a little brother he never had. He hated having to lie but it was for there own safety. Judy's voice caused him to look up.

"I remember like it was yesterday," she said, "John had run away from home. He was only nine and had no other relative near so he ran for about two blocks and then sat down on the sidewalk. That's where I found him. He was shivering and hungry. It was the middle of winter and he hadn't eaten anything."

"Yeah, not my smartest moment," laughed John, "My mom told me never talk to stranger but trust me as a little kid when one offers you food you tend to."

"You're just lucky it wasn't one of those that would hurt you that found you," pointed out Judy.

"True," agreed John.

"Anyway, after he finally went home about a week later he showed up again on my front porch. He had run away again; pretty much after that every time he ran away he ended up staying with me, until he joined the Air Fore.

"Yeah I was the bad child," grinned John.

"Thank you Mrs. Witwicky for the Meal but I need to go," said Mikaela.

"I'll walk you out," offered Sam.

"They sure do grow up fast," muttered Ron.

John response was a simple laugh. They had discussed sleeping arrangements earlier. John had offered to stay at a motel but Judy insisted he stay with them so several hours later found him laying on the couch in the living room. He loved this place but the out of depth feeling he was getting was beginning to bother him. Something was going on here. Ever since Todd had given him the Gift of Life his senses were slowly getting better. The change was almost instant when he finally accepted the gift after year of denying it. Todd had told him his five scenes were now much stronger than a humans but still considerably weaker than a wraiths. He also gained a small amount the wraith telepathic ability allowing his to talk to Todd almost anywhere; an added bonus was he could now activate wraith technology and like Teyla fly the hive ships. But Sam's car, it was a nice car, felt strange. So did Mikaela's toy car. The red Lamborghini, however, just felt completely wrong. Something was diffidently off and John Sheppard was going to figure out why.

Bumblebee wasn't a judgmental being and he knew Sam liked his Uncle, heck so did he but Sam's Uncle, John, was an oddity in and of himself. No one noticed but Bee did. The whole time that man was around him he appeared relaxed but he wasn't. He was forcing himself to relax. Bumblebee could only guess that's what let him notice the Deceptican that tailed them all day. Of course he probably thought it was an ordinary car. But the look he gave it was unsettling. He had told Optimus as much in his report. Uncle John, as Sam called him, was military, but he was off duty now. So why was he acting like something was out to get him? The weird part was he only acted that way when he was near Bee and it had gotten worse when the Decepticon had decided to pull up right behind him. It had been taunting him but Bee didn't fall for it. He couldn't, he had to protect Sam and his family. Lennox said it was probably post-deployment jitters and Optimus agreed but told Bumblebee to keep an optic on the Colonel. Something Bee was more than happy to do.

Mikaela arrived the next morning shortly before breakfast. After they were done the three of them decided to hit the other side of town.

"Yeah they build a Golf course and some basketball courts there a couple of year ago," explained Mikaela.

"Lets go check it out," said Sam.

The three of them ended up shooting hoops and John taught them how to play golf. They spent most of the day there before stopping at a burger place to eat. On the way home the Lamborghini fallowed them again, but only Sam saw the Black GMC Truck fallowing it. After they got home John went to nap on the couch, while Sam spent some quite time with Mikaela.

* * *

Please kindly leave me a review, pretty please?


	3. Chapter 3

Disclamor: I own nothing.

_**Flash Back**_

_t__hought_

Telepathic Talk

I also thank Botosphere for the use of their idea in the fanfiction Kinship. The idea belongs to them. I will also make some small refrences to their story and would recomend it to anyone. the story also has a segual called 'The Ties that Bind'.

* * *

Chapter Three:

He liked this place; a nice grassy hilltop next to a river. If this place was real, he'd imagine there'd be birds chirping in the trees and animal around the water. He was leaning against the trunk of a large tree enjoying the sunshine. John didn't even flinch when he heard the sound of shuffling grass, or the familiar chuckle.

"Are you enjoying yourself, Sheppard?"

"Hey, Todd," said John as he opened his eyes to look at the wraith.

The first time this had happened he had panicked. He had feared Todd could read his mind, but he later learned he could only if John allowed him to. It had been awkward talking to Todd like this at first, but it was like talking in real life. He also figured out that the when he and Todd were near each other, he could talk to him telepathically while awake, which helped when they were in a fight.

"What brings you here?"

"You are bothered by something," Todd stated.

"You picked up on that, did ya?"

"Are you not happy with your family?"

"No it's not them. It's hard to explain and you'll think I'm crazy,"

"And here I thought you already were," chuckled Todd.

"Smart ass," replied John, "Well, you see, my nephew has this car; it's a nice car, but something doesn't feel right about it. I don't get an evil feeling from it, far from it actually. I feel like I can trust it, trust it to keep Sam safe, but it's a car and cars can't protect you."

"I see. You feel like you can trust it like you would trust another person," said Todd.

"Yes," answered John, "Not only that, but there was this red Lamborghini that followed us when we went out and the feeling from it was just pure evil. I felt like if it could grab us, it would kill us all. The feeling got worse the closer it got to me. Plus there was this toy car that felt kind of neutral; somewhere in between the other two."

"The Gift of Life has made your senses stronger. You are now more perceptive to the things around you. I have no doubt that you are sensing something, but I am unfortunately not familiar enough with your planet's vehicles to tell you what you be sensing," said Todd, "However, I do suggest that you follow your instincts on this matter. You believe you can trust the one belonging to your nephew, so trust it. The other one I would stay away from as best you can."

"Don't worry about that, I will. If I have any say in it, I'm staying as far away as possible from that Lamborghini," said John.

"I apologize that I could not have been of more help," sighed Todd.

"It's fine. Hey, listen, I'd better go before my nephew has a heart attack, he's been trying to wake me up for two minutes now," said John.

"Until next time then."

"See you later Todd," waved John.

* * *

"Oh, thank god," sighed Sam when John finally woke up.

"I'm up, I'm up," yawned John.

"Mom wants us to get some things at the store," explained Sam.

"Ok. Where's Mikaela?" asked John

"She went home."

John followed Sam out to the car. He looked at it before getting into the passenger side seat. It wasn't evil; besides, Sam had been driving this car for almost three years now. If something was going to happen, it would have already. The trip to the store was uneventful. They had parked and went in to get what Judy had wanted and then a little more. They were having a half-off sale on candy bars and chocolate was the best cure. They almost made it to the car before John stopped walking.

"Is something wrong?" asked Sam.

John didn't answer him; he couldn't. Fear and terror welled up inside of him. They weren't new emotions; he felt them when getting captured by the Wraith. It wasn't the kind of fear when you were afraid, but then you were scared for someone else. The source was getting closer and fast. He could feel evil, hatred, malice, and every other negative emotion coming towards him form above. Wait … not him…Sam!

"Uncle Jo…" began Sam, but was cut off when John latched a hold of him and began dragging him away.

Sam was about to protest, but the ground where they had been standing suddenly exploded into flame. Both he and John looked at the place before John Suggested,

"We should run."

"Y-yeah," stuttered Sam.

They took off down the lot. They made it to the road before the red Lamborghini that had been tailing them the last couple of days come around the lot and skidding to a stop in front of them. John pushed Sam behind him.

"We need to get out of here," urged Sam, but he plea fell on deaf ears.

The engine of the car revved and John got ready for anything. No amount of preparation could have gotten him ready for what happened next. The car revved again and then it moved, in all directions. It might not have worried John so much if wasn't for the fact the damn thing was looking at him.

"Holy…" was all he could manage before Sam took matters into his own hands and yanked him backwards.

They took off running, Sam further ahead this Uncle. The Decepticon jumped, landing between Sam and John. Sam stumbled forward and fell; John had barely managed to keep his footing before grabbing the gun in the holster on his ankle and opening fire on the Decepticon, it, however, did nothing good other than piss it off. The Decepticon turned its red eyes on John and began walking towards him.

Sam had wanted to keep his Uncle out of the war he had found himself in. He had dragged Mikaela and his parents into it, then Leo two years later. He couldn't do much, so he did the one thing he could, "Bumblebee!"

John had heard Sam shout but was to busy to tell what he had said. He heard the sound of a car engine and saw his nephew's car headed straight for them. He was about to shout to Sam, fearing he would get hit since it was getting closer and not slowing down at all. About the time it would have hit Sam, John saw no one driving. The car did as the other had, changed. Bumblebee jumped and tackled the Decepticon, managing to roll just right so Sam's uncle would not get crushed. He pushed the Decepticon, Breakdown, back away from Sam and John. He felt sorry for John like he had for Sam; finding out about him like this really couldn't be easy.

"Are you ok?" asked Sam.

"I think," was all John could manage.

"I'll explain later," said Sam.

"You'd better," said John.

Sam and John both looked when Bumblebee made the slow approach in their direction. He didn't want to scare Sam's uncle; the man still had a gun. It wouldn't penetrate the outside of armor, but getting shot was still not on Bumblebee's list of things to do today. Bumblebee stopped in front of them.

"You ok Bee?" asked Sam

"Yes," answered Bumblebee this time in his normal voice, "The Decepticon escaped."

"That's ok, he shouldn't bother us again," said Sam, "Bumblebee meet my Uncle John; Uncle John, this is Bumblebee."

"It's wonderful to meet you," said a British accented man.

John couldn't help but smile, "hi."

"He likes to play clips and stuff over his radio," smiled Sam, "When I met him he couldn't talk, so that how he managed to communicate."

"Ahh… I believe we might want to get home before you mother come looking," suggested John.

Sam groaned, "She'll kill me now."

"Why?" asked John.

Bumblebee transformed back into the alternate mode and Sam and John got in. He took of driving himself while Sam pretended to drive.

"Well you see, she kind of knows. So does Dad. Dad's not as bad, but Mom hates them, though not as much as she use to. She was concerned for me, and didn't like the whole idea of me hanging out with aliens." explained Sam, "So; she made both me and Mikaela swear not to say a thing about aliens to you.

"Message form Starfleet, Captain," sounded over Bumblebee's radio about the time a Chevrolet Beat and Trax appeared on each side of the Camero.

"Look like the greeting party's here," sighed Sam.

The two Chevrolets followed the Camero all the way. Sam turned onto his road where John saw a black GMC truck and a blue and red Peterbilt diesel truck sitting on the side of the road by Sam's house. Standing in front of the two trucks were Mikaela, a man in an army uniform, another guy, a kid about Sam's age and bother of Sam's parents. Ron was unhappy and Judy was very pissed off. She was alternating from yelling at the guy in the uniform to screaming at the peterbilt diesel. When Sam and John got out, Judy stopped yelling and practically mugged them.

"Oh god, I was so worried," she half sobbed, half growled.

"Let them go, Judy," sighed Ron, "You're going to suffocate them."

She released the two before going to sob quietly into Ron's shoulder. However, when Judy released them, Mikaela pounced on Sam, hugged him tightly then slapped him, causing John to wince.

"How dare you not tell me that a Decepticon had been following us, or for that matter, why didn't you tell me you saw Lennox at the mall?" demanded Mikaela.

"Look, I'm sorry, ok?" said Sam, "I was angry. I'd finally got to get some normal time and then it was interrupted."

Mikaela just looked at Sam before hugging him again. By this time the other three had walked up to them.

"Are you alright, Sam?"

"Just peachy Leo, just peachy," answered Sam sarcastically.

"We need to go, cube-brain."

"Seriously, Simmons, can't any of you leave me alone?" asked Sam.

"Not when you're on the Decepticons' most wanted list."

"Hey, where the hell do you think you're taking Sam?" demanded John.

"Some place safe," answered the uniformed man.

"Not without me, you're not," stated John, "I don't know any of you, so if you think I'm letting you take my nephew anywhere, then you have another thing coming."

Before Lennox could protest Sam added, "Besides, the Decepticon saw Uncle John with me, which could make him a target."

"Fine," Lennox growled.

Ron took Judy back inside while the others loaded up; Leo, Simmons, and Mikaela road with Bumblebee, while Lennox, Sam and John were to ride with Optimus.

"So, Sam, I think now you be a good time for that explanation," said John

Optimus, sensing Sam discomfort, decided to intervene, "I apologize that you had to be drug into this."

John looked at the dash before looking at Sam, "He's one to, isn't he?" and was answered by Sam's nod.

"Yes, I am like Bumblebee. My name is Optimus Prime and I am the leader of the Autobots."

"John Sheppard, call me Sheppard."

"Very well, Sheppard," replied Optimus, "As to you explanation; we are autonomous robotic life forms from a planet called Cybertron, we came here looking for something called the All Spark. Our planet was once a powerful empire, peaceful and just until we were betrayed by Megatron, leader of the Decepticons. All who defined them were destroyed. Our war finally consumed our planet and the All Spark was lost to us. It eventually found its way here, where Megatron followed it. Megaton had crash-landed in the arctic where Sam's great-grandfather, Captain Witwicky, found him. Captain Witwicky accidently activated Megatron's navigation and the location of the All-Spark was imprinted on his glasses. We, the Autobots, came later and discovered Sam was in possession of the glasses. We managed to locate the All-Spark, but it was destroyed. Unable to rebuild our planet, we stayed here and have been working with your government in a classified project called NEST to eliminate the remainder of our Decepticon enemies."

"Wow," whistled John.

The explanation had lasted most of the trip, so they soon arrived at a private airstrip where two C-17's and more soldiers were waiting. They all had the same symbol that was on Lennox's uniform, so John guessed that was the NEST symbol.

"Look like you brought along an extra," grinned Epps when John go out of the truck.

"Didn't have time to argue," said Lennox.

"He find out the hard way?" asked Epps

"Yep, Sheppard this is Sergeant Epps, Epps this is John Sheppard," said Lennox.

"Pleasure," greeted Epps, "We're ready to depart."

The Autobot with, the exception of Optimus, loaded onto one plane while the others loaded up on the remaining one. John had asked where they were headed, but Lennox and Epps didn't answer. About a couple hours in, John managed to get it out of Simmons. Diego Garcia, that's where they were headed. When the plane landed, Sam offered John a tour, but Lennox said it would have to wait. There was some paperwork that needed to be filled out first.

* * *

Please leave me a review, pretty please?


	4. Chapter 4

Disclamor: I own nothing.

_**Flash Back**_

_t__hought_

Telepathic Talk

I also thank Botosphere for the use of their idea in the fanfiction Kinship. The idea belongs to them. I will also make some small refrences to their story and would recomend it to anyone. the story also has a segual called 'The Ties that Bind'.

Al-Sharif belongs to Botosphere and the mention of leo's postion also belongs to Botosphere.

* * *

Chapter Four:

He wasn't going to tell his uncle about the spark-bond. He wasn't going to tell him about his position among the Autobots. His parents and Mikaela knew. Lennox knew too and, no thanks to the twins, both Leo and Simmons knew. No one else did, not even the government or those in charge of NEST. Optimus told him that it was his choice to tell John and that he would honor it, whatever it was, but Optimus had also pointed out that John did have some right to know just like his parents had. Yeah, well, he wasn't going to, not as long as Sam Witwicky was alive.

_**Sam liked these dream lands because he could talk to Optimus face to face.**_

"_**He has a right to know," started Optimus, "he is, after all, your uncle."**_

"_**And?" asked Sam, "I've managed to drag everyone I know into this war and I refuse to drag my uncle into it for as long as I can."**_

"_**I fear he is already a part of it," sighed Optimus.**_

"_**No. Not yet," said Sam, "He's safe as long as the Decepticons believe he knows nothing; which is why we're not telling him anything."**_

"_**No one is truly safe from the Decepticons," replied Optimus.**_

"_**All I want is a normal relationship with my uncle." huffed Sam, "Is that to much to ask?"**_

"_**Very well, Sam," said Optimus, "I will not tell him unless I have no other option."**_

"_**Thanks, Optimus," grinned Sam.**_

Lennox had given John the tour while Simmons giving John the ends and out of NEST and what it did. Lennox had waited on introducing John to the Autobots. Sam had insisted that he wanted to be the one to do it, but had to go to a meeting with the NEST officials. He had heard from Optimus that many of the Autobots were interested in meeting the infamous uncle of their human Prime and that they had been trying to get info out of Bumblebee; apparently Arcee and the twins where the main culprits. The trio met up with Mikaela and Wheelie, who followed them to the Autobots' hanger where Sam and Leo stood waiting. Leo was forced into the meeting with NEST since he had been dubbed Sam's official human bodyguard. When Leo was given that position he nearly killed Sam.

"Hey, Uncle John," greeted Sam.

"Hey, sport," grinned John.

"Ready to meet the Autobots?" asked Sam.

"As ready as one can ever be to meet giant robots," said John.

The two of them went into the hanger, but then the others went to follow Lennox held them back.

"Let then have some alone time," explained Lennox when he was shot questioning glances, "This can't be easy for either of them."

"You're right," agreed Mikaela while Leo nodded. They followed Lennox from the hanger.

When John entered the hanger he saw the Peterbilt Diesel and Sam's Car. He also recognized the Green Chevrolet Bet and Red Trax that had followed them back to Sam's house and the black GMC Topkick truck. Joining them was a Chevy Volt, Corvette, Hummer H2 and a Motorcycle.

"Hey, guys," called out Sam.

For a moment, John was a little worried but the vehicles all began to move and transform to the bipedal forms of the Autobots. John had only seen Bumblebee transform. He had also had a conversation with Optimus Prime, but he could never have guessed that there had been so many here. It also bothered him that he had never heard about them or NEST before.

"This is my uncle," continued Sam once they finished, "John Sheppard."

"Greetings once again, Sheppard," said Optimus.

"Hi," replied John.

"My I introduce Ironhide, my weapons specialist, and my medical officer Ratchet," said Optimus as he indicated to the two standing next to him, "The others are Arcee, Sideswipe and Jolt; as well as Bumblebee whom you have already met."

The responded with a nod like Ratchet and Ironhide had. Both Sam and Optimus had asked them to not act rashly. They knew Sam had wanted them to be kind to his uncle. Al-Sharif, Sam's aid, arrived to take him and John to see some higher ups who wanted to see them. Bumblebee transformed and gave them a ride to the main building.

"So that's the man Bumblebee was concerned for," muttered Arcee.

"He doesn't seem like much," said Ironhide

"I have to agree with Bumblebee," grunted Ratchet.

"How so?" asked Optimus

"I did not have enough time but my scan revealed something most concerning," Said Ratchet, "the pulmonary scan allowed me to detect foreign elements in his DNA."

"Foreign how?" asked Optimus.

"As of now I cannot tell you anymore without a more detailed scan and for that I will require assistance," said Ratchet.

"I will speak with Sam," assured Optimus.

* * *

"Would you two stop? You're making it hard to concentrate!"

"He started it," said Ronan.

"With you two around, it's like taking care of two children!" complained Rodney.

"Do not worry. John is fine," assured Teyla.

They had not been given any information other that John had disappeared after an accident in the town where his family lived. Ronan, of course, was trying to find someway to make this Todd's fault. The two of them had learned to tolerate each others' presence and, much to their dismay, made a good team.

"He was fine the last time I spoke with him and I can still sense his presence," said Todd, "But I cannot pinpoint his exact location."

"I'm sure he is fine," said Teyla, but her fear was growing as each second ticked by.

* * *

"My uncle's what?"

"Ratchet has detected something in his DNA that he cannot identify and needs more time to run a full scan," said Optimus.

"Why did Ratchet scan my uncle in the first place?" asked Sam a little unhappy.

"He does this with all humans he meets," explained Optimus, "He did the same thing to both you and Mikaela."

"OK," sighed Sam, "What do you mean by cannot identify?"

"As of now I cannot tell you much but Ratchet says he needs more time," replied Optimus.

"I'll see what I can do," sighed Sam again.

* * *

Teyla's patience was wearing thin. They had not heard anything for two days. Todd's inability to locate John only made it worse. General O'Neill was trying his best, but with no evidence it was hard to know where to look. He also did not have much time because the IOA had been hounding him about something else the government was working on. She hadn't had much time to talk to him because a man by the name of Theodore Galloway was demanding to see him that very intent.

"Can't you telepathically call him or something?" asked Rodney.

"It as not as easy as you seem to think, Dr. McKay," grunted Todd, "I have to locate his mind and then make a connection. Without knowing where Sheppard is, I cannot properly do that."

"I thought you could always find his location," said Teyla.

"Normally, yes," said Todd.

"He's around something that can block Todd mental abilities and the gift of life bond thing?" observed Rodney, "Thank can't be good."

Ronan grunted in agreement.

* * *

"Not really, no," said John.

He could not believe that Sam had suckered him into playing a round of twenty questions with the Autobots. With all the questions Bumblebee, Arcee and the Twins had managed to come up with it was more like a round of a thousand questions. Sideswipe had made the comment that he should run for his life and now John was starting to agree with him. Optimus Ratchet and Ironhide stood in the Back, clearly amused. John had learned that the only humans that the Autobots ever truly have any form of contact with were the ones who worked here at the base and out of all of them there where only certain ones that they would prefer to talk to; talking to the same few people had to get pretty boring after three years. The younger ones, who now bombarded him with questions, always found it entertaining to talk with someone new.

"Soes, this golf a yours, it anything' like foosball?" asked Munflap.

"Football," said Sam when John looked at him.

"Ahh… no, according to a friend of mine, it's boring," laughed John, "But I'm told Hockey is interesting."

"Yeah, sure it is, if you like watching guys beat the living shit out of each other on ice with sticks," chuckled Sam.

After enough pestering from Arcee, John finally explained in more detail about what Sam had said along with every detail he knew about Hockey.

"Autobots, enough," said Optimus, "It is getting late and Sheppard and Sam need to get some rest."

"Uncle John, you go ahead I need to ask them about something," said Sam.

"Alright Kid, I'll see you later," smiled john and ruffled Sam's hair who swatted his hand away.

"What have you got?" asked Sam when John was out of ear shot.

"Many things, Samuel," replied Ratchet, "and I fear you will not like any of it."

"Spit it out already," said Sam growing impatient.

"I have managed to isolate two distinct sets of Nitrogenous bases. One set is human, however upon further research has only been found in about .00005% of your worlds population and the other…" paused Ratchet.

"What is it, Ratchet?" asked Optimus.

"The other set is not human," continued Ratchet, "I have never seen anything like it before. They show traits of distinctly insect DNA."

"Are you saying my uncle's part bug?" asked Sam.

"no, but the traits are still there," said Ratchet, "What concerns me is that there is not possible way for Colonel Sheppard to be born with this as a part of his DNA, nor could he have encountered it on Earth."

* * *

Please leave me a reviwe, pretty please?


	5. Chapter 5

Disclamor: I own nothing.

_**Flash Back**_

_t__hought_

Telepathic Talk

I also thank Botosphere for the use of their idea in the fanfiction Kinship. The idea belongs to them. I will also make some small refrences to their story and would recomend it to anyone. the story also has a segual called 'The Ties that Bind'.

* * *

Chapter Five:

Something was wrong. He knew he was being blocked. It was impossible to tell whether it was intentional or accidental, but either way he could not call his brother. Standing on the edge of the river, Todd could barely see the other side. The river was the bridge and the shores were their minds. From years of experience, Todd knew he had only one chance. One shot to try and reach John, but neither he nor john was going to like it.

* * *

John couldn't see the other side. His friends had to be worrying themselves sick. Since he couldn't tell them the normal way, Todd was going to have to do it for him. John had been at this for an hour and as luck would have it he couldn't find Todd. He could only assume Todd was having the same problem and that's way Todd hadn't found him. Thinking back John remembered something Todd had told him once.

"**The bond produced by the Gift of life can be very weak or very strong," explained Todd, "It depends on the two that share it. The bond also can be strengthened or weekend by emotions,"**

"**Is that good or bad?" asked John.**

"**Both." Replied Todd, "The River is the link and the shores are our minds. Under normal circumstances the other side should be clear and permit us to venture from one side to the other. But should the other side not be clear then there is something blocking the bond. The only know way to overcome that block is to imagine your self in a place that has extreme emotional value for both participants. The place either has to be one of extreme positive emotions or negative."**

"**Like the Genii prison," guessed John, wincing as he said it.**

"**Yes, Sheppard, like the Genii prison."**

John felt wind hitting his back and turned to see an old door. Without him touching it, the door swung open and John was thrown into darkness. Once John got his bearings back he looked around, recognizing the cell instantly. He had never wanted to see this place again, not after what Kolya did to him. He was fed on by a Wraith and his friends were forced to watch. When he had gotten back to Atlantis after the incident he had watched the recording several times. He thought it kind of funny that the Wraith, Todd, was now one of his closest friends. John felt a presence at his back and turned to the window. The very one where he had first seen Todd. He couldn't make out anyone, but a shadow could be seen on the other side.

"Sheppard…talk…listen….missing… cannot… you...unknown….blacked…. looking…cannot…anymore…." The shadow vanished, leaving John alone.

It had sounded like someone trying to talk threw a fuzzy radio. He got the basic idea though. They didn't know where he was, and Todd was having a hard time locating him. His superiors didn't know or weren't telling his team. If he didn't show up when they were to return to Atlantis, he'd probably be marked as AWOL. John was sure they heard about the incident in his nephews' hometown, but he had just vanished of the map; Sam, Mikaela and him. God he hoped nothing bad happened.

* * *

NEST surveillance had detected several Decepticons. They were located in Kadikchan*, a Northern Russian town. The town was now abandoned when the City boiler, which provided heat for the entire town, broke down, possibly in deep winter, causing all the pipes to freeze. The residents started freezing to death, and were subsequently evacuated.

"Why there?" asked Sam.

"Don't know," said Lennox, "wheels up in five minutes!"

John watched while the NEST tem quickly move to depart. He was reminded of his team again. They were so going to kill him. He fingered the necklace he wore. Most people passed it off as some trinket he had gotten from somewhere, but it weren't. It was a subspace radio, a Wraith subspace radio to be exact. Todd had given it to him when he had done a little undercover work for him. You can't pretend to be a worshiper and have an Atlantis radio with you; it would have gotten them both killed. After that Todd had let him keep it. It had only two frequencies set on it. The Wraith one Todd's hive used and the one used on Atlantis. The only ones who knew about it were his team, Woolsey and General O'Neill. Todd had insisted the he only use it in the life or death kind of situations. He wasn't there yet. John was tempted to use now but he waited.

* * *

They had split up; Lennox's team took the north side of town and Ironhide's took the south. Bumblebee had stayed with the twins back at Diego Garcia. Optimus knew Sam was safe back at the NEST Headquarters, but still felt better if an Autobot were with him. He was couched down with Ratchet and Sideswipe behind him. Arcee and Ratchet had gone with the other group. Lennox signaled for Optimus to attempt to come up behind the Decepticon, but it transformed and leapt towards them before he could get close. The deception almost reached them, but Optimus was faster. He used his blade and sliced the Decepticon face in half. A second one appeared and successfully knocked Optimus backwards. Sideswipe ran his blade throw the center of this Decepticon's chest.

"Is that all of them?" asked Lennox.

"I'm not detecting anymore," said Ratchet as he examined Optimus for any serious injuries.

"Lennox," shouted Epps.

Lennox looked up to see black team coming towards them.

"We took out three Decepticons," said Ironhide.

"Yeah, and one of them had this," said Epps.

"What is it?" asked Lennox looking at the bluish device.

"I don't know," replied Ironhide, "I've never seen any think like it before."

"Nor have I," agree Optimus.

* * *

Todd opened his eyes to see Teyla staring down at him.

"Are you alright?" she asked.

"Yes," replied Todd.

He pushed himself up and notices he was still in the labs. Both Dr. McKay and the Runner were still present. Rodney was typing away at the computer he sat at while Ronan stared at his back causing the scientist to fidget.

"I was unable to locate him," sighed Todd, "However he is fine and appears unharmed.

Ronan and Rodney both stopped and looked at him. Rodney let out a sigh of relief. Ronan's solemn mood appeared to lift and Teyla just nodded.

"It is good to know he is at least fine," said Teyla.

"Agreed," replied Todd.

* * *

Lennox had retuned twenty minutes ago.

"What is it?" asked Leo.

"I don't know," grunted Lennox for the hundredth time.

"Sir," said a soldier, "Mr. Sheppard has asked to see the device."

"Why would he want it?" asked Simmons.

"I don't know but Mr. Witwicky, Optimus and Ratchet were with him."

"Alright, let's go see," said Lennox.

* * *

It was a Wraith data storage device. John stared at it. _Why the hell did a Decepticon have this?_ Lennox entered with Leo and Simmons. He had some words with the guy who had been studying it before turning to him and Sam. Ratchet was the only other Autobot present. He had been running scans and so far all he could come up with was that it was composed out of some organic based material. Ratchet looked at the Colonel who held the device and at it a couple of times before he was sure.

"Pardon me, Colonel," said Ratchet," But I could not help but notice that the device and your necklace have the same organic type of composition."

John's head shot up. The assembled solders and Autobots looked the Colonel. John sucked in an air full of longs and before Sam could ask him about what Ratchet meant he was gone. All John heard were the startled shouts and the wind rushing past his ears. He knew the Autobots could catch him with ease but he still ran with all his might. It took Lennox a second to register what happened, but he was soon shouting orders to catch Sheppard. Sam was equally as surprised. He knew Optimus felt his shock and fear. One second John had been standing right next to him and the next he was running for dear life. When they caught up to him he was surrounded by NEST solders, which had their guns leveled at his Uncle's chest. Sam arrived in time to see John disappear in a white light.

"What the…" began Lennox.

"It would seem that Sheppard has teleportation technology," stated Optimus.

"But how?" asked Sam

"I do not know."

* * *

John found himself facing stars.

"Welcome, Colonel, to the Odyssey."

"Thank you, Colonel Emerson," replied John, "Now if you could beam me to the SGC."

"Certainly, Colonel," said Emerson.

* * *

John appeared in the gate room at the bottom of the ramp leading to the Stargate. He only managed to make it out before Teyla collided into him, Rodney and Ronan behind her. Rodney was breathing heavily. They had obviously run when they got word that he was beaming to the SGC. Todd came up behind them at a much slower pace. He wasn't much on running unless he really had to.

"Where have you been?" demanded Rodney.

"Busy," grinned John, "I brought you a present."

John pulled out the wraith device and tossed it to Rodney whose eyes widened to the size of dinner plates. Rodney flipped it over several times before looking a John again with disbelief.

"Where did you find this?" he asked.

"You wouldn't believe me," john grinned.

Before they could continue General Laundry approached them telling them that General O'Neill wanted to see him. They entered the briefing room to see O'Neill up on a video feed.

"Where the hell a have you been Colonel?" demanded O'Neill, "and don't give me a smart ass answer."

"Diego Garcia, Sir," replied John.

O'Neill's response was to chock on the coffee he was drinking. "Diego Garcia?"

"Yes, sir," answered John, "I don't suppose the name Major William Lennox means anything to you?"

"Colonel, do you know how hard it is to keep the SGC and NEST out of each others' hair?" asked O'Neill

"I'm sure it's not easy, sir, but on NEST's most recent mission one of the Dec… targets had a Wraith storage device on them. It was found by Sergeant Epps," explained John.

His team was confused, but aware that they had missed something.

"I was forced to use the radio Todd gave me when one of their assets concluded that the device and the radio were mad out of the same thing," continued John.

"That necklace thing you wear," asked O'Neill

"Yes, sir."

"It would appear Colonel we have a serious problem. What do you suggest, Colonel?" asked O'Neill.

"A joint operation between NEST and the SGC until the specifics can be determined," stated John.

"Your recommendation has been noted, however, I must speak with the NEST advisor first," said O'Neill.

"Do I have permission to give full disclosure to my team?" asked John

"Yes, Colonel, you do," replied O'Neill, "In all technicalities the Stargate Program outranks the NEST program in security clearance so you good to go on that part. I want you and your team to be ready to depart as soon as I get the go ahead."

"Yes, sir," said John.

* * *

Lt. Colonel John Sheppard was a disaster zone. If something bad was going to happen, he seemed to always be at the epicenter of it. Jack had to have a word with Defense Secretary Keller. He himself didn't have any control over NEST, but he did know about it thanks to his position and ten years of fighting the Gou'uld and the Ori. He was also responsible for keeping the SGC out of NEST jurisdiction. Keller did the same thing for NEST. He also knew about the SGC and the Atlantis expedition, but had no control over it. He just kept NEST out of the SGC's hair. Jack knocked on the door. He pushed it open to see Keller at his desk.

"John," greeted O'Neill

"Hello, Jack," smiled Keller, "What can I do for you?"

"It would seem my Atlantis Military commander has gotten involved with NEST," sighed O'Neill.

"How?" asked Keller.

Jack explained everything he knew about the situation, witch wasn't much. Keller listened only asking a few questions.

"Do you agree with Colonel Sheppard," asked Keller.

"Yes," replied O'Neill, "we have too many unknowns. While we know a small number of wraith escaped when the Colonel's team blow up the Super-Hiveship they have remained inactive. We cannot have Wraith and the Decepticons form an alliance. Not only could that raise the chance of more Wraith getting here, but it could also strengthen the Decepticons."

"So then we agree," said Keller."

"Myself and Colonel Sheppard will accompany you to Diego Garcia and once the situation and full briefing is concluded we will beam the rest of his team over," said O'Neill.

"Until then, General," replied Keller.

* * *

Please, kindly leave me a review, pretty please?

alright I have one request. I know not everone has an account and I do exept Anonymous Reviews but please if you do leave a review and you do have an account take five second to log in. I do like to reply to some of the review i get and when there anonymous it makes it very hard so please if you can log in. Thank you and havea wonderful day.


	6. Chapter 6

Disclamor: I own nothing.

_**Flash Back**_

_t__hought_

**_Telepathic Talk_**

I also thank Botosphere for the use of their idea in the fanfiction Kinship. The idea belongs to them. I will also make some small refrences to their story and would recomend it to anyone. the story also has a segual called 'The Ties that Bind'.

Sorry, this is a repost. I noticed some errors i had missed before

* * *

Chapter 6

Sam was confused. His uncle had run from NEST and then just vanished. Optimus had tried to come up with explanations, but he was also confused by the events of the last two days. He didn't like the feeling Sam was giving off. Sam's solemn mood and the large amount of unknown information were not making any of the other Autobots feel any better.

"Have you been able to figure out what that was?" demanded Lennox.

"No, Major," said Optimus, "It was some form of subspace teleportation, but I do now know where Colonel Sheppard was taken."

"I was unaware that your people had developed something that advanced," said Ratchet, "It seems there is more about you we do not know."

"We haven't," said Simmons, "There was nothing about that level of tech in any files from Sector Seven and I've looked in every classified file I can get my hands on."

"Something else from outer space?" suggested Leo.

"Lennox, Sam!" shouted Epps from the entrance, "Sec. Def. is here to see you. He wants Optimus to come as well."

After transforming, Optimus escorted Lennox and Sam to the main building. They found Keller having a conversation with a gray-haired man in an Air Force uniform.

"Uncle John's in the Air Force," said Sam.

Lennox sighed, "Then let's see what this is about."

Sam and Lennox walked up to the two men. Optimus waited at the entrance, unsure of the situation. He could read the tension of the room. While Senator Keller oversaw NEST, he never directly interfered unless something dire was afoot.

"Major, Sam," greeted Keller, "This is General Jack O'Neill. He is Head of Homeworld Security. He has helped monitor NEST activity since the beginning."

"General," saluted Lennox, "Pleasure to have you here, but I cannot help to think this is not a social visit."

"Unfortunately not," agreed Jack, "It has come to my attention that you and your team acquired something on your last mission."

"Yes, sir, we did but…"

"But what?" asked Jack.

Optimus, who had rolled into the building, thought this an excellent time to intervene.

"Some complications arose and we unfortunately lost what we found."

Jack jumped. He had known that an Autobot was with them, but to have a diesel engine suddenly speak was still a shock.

"General, this is Optimus Prime," introduced Keller, "Leader of the Autobots."

He looked at the red-and-blue vehicle.

"Now is a good time Optimus."

Optimus took that as a signal to transform into his bipedal form, "Greetings, General."

"Hi." replied Jack, not too surprised, "What do you mean by complications?"

"I believe you should ask Colonel John Sheppard," said Lennox, "He was our complication."

"So you admit he was here?" asked Jack.

"Yes, sir." said Lennox, a little confused, "When Sam here was attacked by a Decepticon we had not choice to bring him."

"He was with me during the attack," continued Sam, "They saw him with me. My parents have already been abducted because of that same reason, I couldn't let Uncle John be abducted too."

"I think he would have been just fine," muttered Jack, "Please follow me; you too Optimus."

They followed the General to a large room with a table on a raised up platform with a large TV screen imbedded on the wall.

"He admitted it. You know owe me twenty bucks, pay up Colonel," said Jack once he was on the platform.

Sitting in the chair on the far side near the head of the table was John Sheppard. Optimus was pleased to feel the feelings a happiness wash over Sam. Lennox, however, was less than happy to see the man.

"How you doing, kid?" asked John as he handed the General a twenty dollar bill.

"Confused," answered Sam.

"I think we're all confused," said Leo.

Leo, Simmons, Michaela, and Epps stepped onto the platform. The Platform was level with the tall Autobot's chest.

"Now that we are all here, we can get started," said Jack.

Jack sat at the head of the table while Keller sat on his left. John was on his right. Sam sat next to his uncle and Michaela sat next to him. Lennox, Epps and Simmons sat down on the left and Leo, next to Michaela. Optimus stood next to the platform, behind Sam.

"Alright, what I'm about to tell you is classified," said Jack, "Now what you found was this."

Clicking a remote the screen sprung to life. An image of the wraith storage device was now on the screen.

"This is a storage device, more importantly this device contained Intel. Intel we needed," continued Jack, "The appearance of this device and how a Decepticon got a hold of it is much more troublesome."

"General, said Optimus, "My medical officer and several NEST scientist were unable to determine what this was, how is it that you know so much about it?"

"I agree with the big guy on this," said Lennox.

"The storage device is not the first one we've gotten a hold of," said john, "They are made by a race know as the Wraith."

"You have encountered other Alien races before?" asked Optimus.

"We have?" How come Sector Seven didn't know about them?" demanded Simmons.

"During a dig in Giza in 1968 archeologist uncovered a stone ring. It was until a man named Daniel Jackson was able to decipher it that we learned what we found."

"Daniel Jackson? Wasn't he the one who said pyramids where ancient alien landing sights?" asked Leo.

"You've read his books?" asked Jack.

"Yeah, Simmons had them," said Leo.

"What, they were interesting!" protested Simmons.

Sam rolled his eyes and Epps chuckled.

"Anyway, the stone ring or Stargate was used by a race know as the Goa'uld. They posed as ancient Egyptian gods. The Stargate was buried by the followers of Ra who fled Earth when his worshipers rebelled. The Stargate was a wormhole device that connects to different worlds. We have used the Stargate for the past fourteen years." explained Jack, "We eventually came across the original gate builders, a race know as the Ancients."

"They all ascended to another plane of existence, but left behind their city, Atlantis. We found that city and for the past six years I have leading a similar program out of Atlantis," said John.

"Hold on, you're trying to say Atlantis is real?" said Epps in disbelief.

"I am familiar with your Earth stories about the City of Atlantis but I have been unable to detect any sort of structure on your planet," said Optimus.

"Atlantis is currently in the Pegasus Galaxy, where we fight the Wraith," explained John, "The Wraith is the race that defeated the Ancients and caused them to abandon the city. The Wraith are a species that feeds on humans. More like space vampires really, except they feed on life energy instead of blood."

"The Wraith has been trying to find earth because there were too many of them and not enough humans to go around; last year they found it. They took a ZPM or Zero Point Module and were able to use it on one of their hive ships, something they couldn't do before and reached Earth. Thanks to the efforts of Sheppard and his team we were able to blow it up, but I believe some survived," finished Jack.

"There is a small chance that they are working with the Decepticons and that is why Colonel Sheppard and his team will be leading a cooperative Mission with NEST until this problem can be solved," further explained Keller, "His team, SGA-1, will be arriving today. They have already had the briefing for NEST."

Passing out folders to everyone Keller began explaining who the profiles were of.

"You'll find information on the team in the folders. SGA-1 consists of five members, unlike the other teams who have four. The first being Colonel Sheppard; the second member is Doctor Rodney Mackey, one of the top experts in ancient technology. The Third is Teyla Emmagan, Leader of the Athoian people. She and Ronan Dex, a Satedan are both natives of the Pegasus Galaxy."

"Why does the last page not have a picture?" asked Lennox.

"I think Colonel Sheppard should be the one to explain him," said Jack.

"Well to put it simple, he's a Wraith," said John, "saved my ass more times than I can count, too."

"A Wraith?" shouted Lennox.

"Uncle John, you said the Wraith were the guys trying to kill you. You also said they eat people," said Sam, "why do you have one on your team?"

"He maybe a Wraith, but Todd has saved me and my team more times than I can remember. He has even done so at the expense of his position as leader of the Alliance and his hive," said John, "Not only that, the Alliance is the strongest Wraith faction right now. We have several advantages with Todd leading it."

"Todd? Is it just me or does that name sound to earthy?" asked Leo.

"It's what we call him," said Jack, "Wraith aren't very forthcoming with their names, if they have any at all, so Sheppard here has named every one that we have ever had prisoner."

"What? I've go to call them something. 'Hey, you' or 'Wraith' gets old after a while," defended John.

Jack just shook his head. Keller had heard about John Sheppard and his infamous naming of Wraith before. Lennox was under the firm belief John Sheppard was crazy, he supposedly fought life sucking aliens in another galaxy on a daily bases and he named them, not to mention has one on his team that he seems ready to defend at a moment's notice. Optimus could not help to feel concerned and in awe of these humans at the same time. Not only had they discovered means for interstellar travel, but have encountered other races before the Autobots.

"General, how many other races have you encountered besides the ones previously mentions?" asked Optimus.

"How many others?" repeated Jack, "Umm…Let's see we have the Nox, Asgard, Tok'ra, Sodan, Hoffins, and Jaffa, all of whom are allies then we have the ones like the Ori, Genii, and Replicators who want to destroy us all."

"Those are just the ones that he can remember off the top of his head," grinned John.

"True," agreed Jack, "I'm sure I'm missing several."

A younger NEST soldier entered the room and whispered something to Keller.

"It seem SGA-1 will be arriving any moment," said Keller, "Colonel, I believe you should go meet your team and the come to the Autobot hanger."

"Yes, sir," said John.

John left the table and jogged out of the room.

"Shall we?"

* * *

Todd could not believe what he had heard; these Earth devices where really Aliens from a planet called Cybertron and they could transform. After a long explanation of who they where, and how they came to be here Todd was growing concerned for this race. Humans-more precisely the ones of Earth-seemed to be getting themselves into all sorts of trouble, even without the Wraith looming over them. While Todd didn't really care much for these humans, they where his brother's people and this was his brother's true home.

"How the hell could they hide something like that?" sounded Rodney's voice, interrupting the Wraith's thoughts.

"Do all of your things on Earth do that?" asked Teyla.

"No!" shouted Rodney, "They're not suppose to!"

"They look cool to me," said Ronan.

"You should feel like kindred spirits runner. After all, you're both homeless," growled Todd.

Ronan glared at the Wraith, before a fight could begin, Teyla, sensing the danger, interrupted, "We are suppose to meet John there and he was to take us to meet the NEST team we will be working with."

"These Autobots, as they are called, may prove to be interesting," nodded Todd, "I also believe they may have been the ones responsible for the block."

"How so?" asked Rodney.

"They are unknown to me; therefore their presence could have proven a hindrance to Wraith telepathy. While Wraith can contact each other over great distances, a Stargate's activation has been proven to throw it off if the distance is too far," explained Todd, "The energy these beings run off of has to be more powerful than that of a Stargate and with so many in one concentrated area so close to Sheppard made it impossible to communicate."

"I guess that makes sense," said Teyla.

"It does?" muttered Rodney.

"We're landing," said Lorne.

"Thank you, Major," nodded Teyla.

* * *

The plane landed without any difficulty. Major Lorne had come along for both the fun and to help keep an eye on Todd. John knew Lorne trusted Todd as much as he did, but this was more for the protection of Todd than any thing else. John knew that Lennox was going to insist that Todd have a guard at all times, so why not have someone he was familiar with? Plus, one who knew Todd's boundaries and would not overstep them. Besides, Todd liked Lorne and Lorne liked Todd. They had actually gotten in a conversation once on the difference between Human and Wraith art back when Lorne still had to guard the Wraith on Atlantis.

The rear hatch opened and His team exited the plane. Most of the NEST soldiers had been informed of their current predicament so the arrival of the team wasn't a shock, but the site still shocked many people.

"Have fun?" asked John.

"If you consider fun to mean sitting on that flying contraption without inertial dampeners for several hours, then yes, Sheppard, we did," replied Todd.

"Bumpy ride, huh?" grinned John.

"Yeah," said Lorne

"Hey, Sheppard, look at this," said Rodney shoving a tablet in his face.

"What am I looking at?"

"The information on the Storage device," said Todd.

"I was able to gain access to it and guess what I found… There are a lot more Wraith here then we thought," explained Rodney.

"But I and Todd are still unable to scene any," said Teyla.

"Twelve darts survived and each dart had about five drones in the buffer, plus the pilots so we are looking at about 72 wraiths on Earth at max," said Rodney.

"How the hell haven't we been able to locate them?" demanded John, "That many Wraith and not one old mummified body!"

"I agree, while Wraith can go a while without feeding, some evidence should have turned up by now," Said Todd.

"It's a bit unnerving, Sir," agreed Lorne.

"Well, no sense in worrying about it now. We have some guys and alien robots to meet," grinned John.

* * *

Lennox had been informed when the plane had landed. The people who go off were described as followed: short, pretty, large, military and creepy. Lennox assumed that the short talking was the scientist, pretty was probably the woman Teyla. The large one was probably Ronan Dex and creepy _thing_ was most definitely the Wraith. A sixth man was reported with the group as they approached the hanger.

"Sir, I'm told someone who wasn't in the briefing file was with the arrivals," said Lennox.

"That would be Major Lorne. He is Sheppard's CO2. He came along to keep an eye on Todd," explained Jack.

"If you trust this Wraith so much, then why does he need someone to keep an eye on him?" asked Simmons.

"I asked him to come along," said Keller, "I heard that he was the one who guarded the Wraith during his first visits to the city. I felt it would be better for someone who was familiar with him to pose as a guard. I'm sure Major Lennox would have had a guard posted on the Wraith while he was here."

"Yes, sir, I would," agreed Lennox.

"Am I the only one who still hasn't gotten over the whole life-sucking part?" asked Leo.

"Lay off, will you?" ground Sam, "Uncle John seems to trust him, plus we have never met him or any other Wraith so who are we to judge?"

"I agree with Sam. The Wraith are also unknown to us," said Optimus.

"This will prove to be fascinating," said Ratchet.

"Yeah, he won't eat us, but he might eat chu'," said Mudflap.

"Knock it off," said Bumblebee.

"Autobots, enough," ordered Optimus.

Voices where heard approaching the entrance; John was the first to come into sight. A rather pretty woman with dark skin and brown hair was next to him. Next to her was a small pudgier man. Behind him and the woman was a tall man with dreadlocks. Behind john was the greatest shock of all. He was by far the tallest of the group. He also wore what looked like black leather and had white shoulder length hair. He had a star shaped mark on his face surrounding part of one eye. On the other side of the Wraith was a man that had a military uniform on. The patch on the side said Atlantis and had a picture of a Pegasus. The other sleeve had an American flag.

"Guys I'd like you to meet, Major Lennox, Simmons, Leo, my nephew Sam and his girlfriend Mikaela," introduced John, "and these guys are my team, Teyla, Ronan, Rodney, Todd and this is Major Lorne.

After several hellos and nodes to one another Keller spoke, "I am Defense Senator John Keller and I thank you all for coming, but now to get down to business. As you no doubt heard about them from the briefing, I would like you all to meet the Autobots."

Optimus was the first to transform, but the others swiftly followed. He had assumed that the one behind Sheppard was the Wraith and the Colonel's introductions only confirmed his suspicions. After the introduction of each Autobot, it was determined that they would be left to their own devices until Decepticon or Wraith activity was detected.

Rodney glared that the computer. They where already set to detect Decepticon signatures, but he was trying to calibrate it to detect Wraith life sighs as well. Ronan, Epps, and Ironhide had become fast friends. Ratchet had watched and analyzed all five of the new people he had met and had found something most interesting.

"I see," said Optimus.

"Indeed. I was able to determine that the woman, Teyla, was indeed born that way, but Colonel Sheppard was not," said Ratchet.

"What do you mean?" asked Sam.

"Simple Samuel, the unexplained DNA that was unknown is Wraith. It is, in fact, an exact copy of the DNA from the Wraith."

"How is that possible?" asked Sam.

"I do not know," said Optimus, "I fear that is something you will have to ask your uncle yourself."

Sam didn't want to ask. John would know that he had been snooping. He could always blame Ratchet and Sam was sure the medical officer would take the blame, but it was his fault too. He was the one who let Ratchet dig further.

"Hey, kid, what's with the long face?" asked John as he heaved himself up on the makeshift table thing.

Ratchet had built it. It not only allowed Sam to talk better with them was also used be several other trusted humans. It put them on a more eye to optic level than having the Autobots look down and the humans having to always crank their head up.

Todd had chosen to remain by the hanger door. Lorne was with Teyla while, last he saw, the runner and other human was off with the black machine.

"Hey, Uncle John," stuttered Sam, "what're ya doing here?"

"I asked him here, Samuel, I would like very much to talk to him and the Wraith," said Ratchet.

"Hey Todd, come over here already!" called John.

Todd left his spot in the shadows and carefully ventured over.

"Really Todd, you need to stop lurking." said John, "That creeps people out."

"I was not lurking, as you so put it, Sheppard. I also do not care for the opinion of your people."

"Ratchet here wants to talk to you."

Inclining his head to John, Todd turned and faced the Autobot. "We have never encountered your race before and I would…" John tuned the rest out. Looking at Sam he could tell the kid was bothered. He knew they knew he had Wraith DNA. He and Todd had arrived earlier than planned at the hanger and heard tail end of the conversation. John also knew that Sam had served as Ambassador for the Autobots for the last eight months. He chose not to say anything, though. It was Sam's life and he would tell him when he was ready.

* * *

please leave me a review, pretty please?


	7. Chapter 7

Disclamor: I own nothing.

_**Flash Back**_

_t__hought_

**_Telepathic Talk_**

I also thank Botosphere for the use of their idea in the fanfiction Kinship. The idea belongs to them. I will also make some small refrences to their story and would recomend it to anyone. the story also has a segual called 'The Ties that Bind'.

Here is Chapter seven. Sorry it took so long, been doing other things. I will try to get chapter 8 up as soon as possable but i'm working on this and three other fanfictions so who knows when this will get updated. I have not abandonded it and never will, i like it too mcuh to do that.

* * *

Chapter 7

John heard Rodney and Todd arguing with tired amusement. It wasn't really an argument though. Rodney argued while Todd glared; this led to Rodney wanting to sink through the floor. Todd wouldn't hurt the scientist; both John and Rodney knew that. John could remember when Todd admitted his growing fondness for the scientist, but that didn't make the Wraith any less scary. Lorne sat next to John, watching with the same amusement.

"Enough," groaned John.

"He started it." was about to leave Rodney's mouth, but one last glare from Todd made it come out as a squeak instead.

"What are you arguing about, anyway?"

"Dr. McKay cannot collaborate this to locate Wraith."

"That's not the problem," protested Rodney, "This locates Decepticons using thermal scanners."

"How is that a problem?" asked Lorne.

"A Wraith is only a few degrees cooler than humans. As your technology cannot tell the small difference, humans and Wraith will appear the same," explained Todd.

"Now what?" John asked.

"Given enough time I can build a module that will locate the Wraith and Decepticons."

"I'll call General O'Neill and see what he can do."

John left Todd on the phone with the O'Neill to explain what he would need. John went in search of Sam.

* * *

"They gave you that much?" Lennox asked.

"I was surprised as well," replied Ratchet.

Lennox, Sam, Leo, Simmons, Mikaela and the Autobots stood in the hanger and listened to Ratchet as he shared the information he had been given by both Homeworld Security and John and Todd. He created human size holograms on the table as he explained.

"These are called Drones. They serve as the foot solders. The mask-less Wraith are the ones who control them. They vastly outnumber the Commander Wraith. Wraiths live aboard ships. These Hive Ships are each ruled by a singles Queen."

"What weapon capabilities are the Wraith capable of?" asked Lennox, "That's something we need to know if we want to fight them."

"The ships have energy based weaponry; the smaller cruisers are the same. The smallest ships they have are Darts and are energy based as well. They are designed for travel trough a Stargate. Their Hyperspace engine travel is limited. After a certain distance they must allow the engine to recharge before activating it again."

"And the Wraith themselves?" prompted Simmons.

"They carry Stunners. The Drones have a rifle type while a Commander would carry the much smaller handheld version. The weapons deliver a shock to the targets nervous system, rendering them immobile."

"What good is a weapon if it only stuns them?" asked Leo.

"A Wraith would take the stunned person, presumably to feed on them. According the Colonel Sheppard, a Wraith Hive will cull a planet, capturing many people. Those who are not used as food are turned into worshipers."

"That's horrible!" cried Mikaela, gripping Sam's hand harder.

"That why we fight them."

"Colonel," acknowledged Simmons and Lennox.

"Uncle John," greeted Sam.

"Rodney says your system can't be altered to locate Wraith."

"Can't you just alter the thermal scanner to locate Wraith?" asked Epps.

"Nope; Wraith are too similar to humans in body temperature for it to be able to tell the difference. We'll get Wraith and every other human on the planet," answered John.

"I was afraid of this," said Optimus.

"You were?" asked Sam.

"According to the information Ratchet has obtained, the Wraith evolved from a species of insect in the Pegasus Galaxy. This insect fed upon humans and over the course of thousands of years began to take on human characteristics, slowly evolving into the Wraith as we would know them today," replied Optimus.

"Very nasty bugs," added John

"Then how do you plan on locating the Wraith, Colonel?" asked Lennox.

"Todd says he can build one that will be able to locate both Wraith and Decepticons in a matter of hours. General O'Neill will beam over anything he'll need."

"Colonel, as a matter of personal interest, how does on befriend a Wraith?" asked Simmons.

John went rigid, he had expected someone to ask him about how he had met Todd, but he had hoped it wouldn't be this soon. It wasn't Todd's fault, he knew that, but some people on Atlantis still blamed the Wraith simply because he was Wraith. John didn't; they had both been prisoners and in the end he did help him escape, even at the cost of his own life; though at the time it was simply out of self preservation. It wasn't his fault.

Sam saw his Uncle go rigid, the memory must have been a painful one. He too had wanted to know the answer to that question, but not at the expense of his uncle's pain.

"I'm gonna go check on Ronan and Teyla," smiled John.

"Did you notice?" asked Lennox once the Colonel left.

"Yeah," replied Simmons.

"Notice what?" asked Leo.

"He was touching his chest, the center," answered Lennox, "I doubt he even realized he was doing it."

"How could you ask him something like that?" asked Sam venomously.

"It is a valid question, Samuel," said Ratchet, "Knowing what we know about the Wraith and their low opinion of Humans, one would wonder how a human would become friends with a Wraith."

Sam glared at the Medical Officer, surprising everyone. The look he had given him was one that no one had ever seen Sam give to any of the Autobots during the whole time he had known them.

"Sam," consoled Optimus, "We meant no harm to your uncle and if you wish, we will not speak of this again."

"No… I'm sorry. You guys did nothing wrong. I just overreacted," said Sam.

Bumblebee watched Sam sadly. He knew why Sam reacted the way he did. He was still upset about all that had happened. First his uncle gets drawn into the Autobots' war and then he finds out that he had been fighting aliens in another galaxy for the past six years. He was hurt that his Uncle had lied to him but understood why, he was happy that he didn't have to lie to him about the Autobots anymore and he was sad because he could never have a normal relationship with the man ever again.

* * *

John flopped into the chair, almost knocking it over. The quiet clank of tools was heard next to him.

"You are displeased."

"I don't want to talk about it."

"You do, Sheppard. You cannot lie to me."

John looked over at the Wraith who was now watching him. Rodney was no doubt off doing something else since Todd probably threatened him with bodily hard if he didn't leave the Wraith in peace to work. Lorne was strangely absent.

"Where did Lorne go?"

"I sent him away shortly before you came. I figured he would prove useful somewhere else."

John chuckled.

"What is bothering you, my brother?"

"Simmons asked me how I met you."

"Ahh… A question I had been expecting for some time."

"So was I, but that didn't make it any less of a shock."

"With all the information we have given about the Wraith, they where bound to wonder how you, a human, could call me, a Wraith, your friend."

"What do I tell them?" asked John, "Lennox and Simmons won't stop until they have answer."

"What ever you wish; I doubt they will ask me and should they, I will not give them the answer they wish."

"I'd expect nothing less from you."

"The computer is functional and already locating three Wraiths near the vicinity of the costal region off the area you call Virginia."

"Virginia?" John shot up from the chair and looked at the screen, "That's a lot of dock warehousing. It was abandoned for a newer facility about fifty miles away."

John told a NEST soldier to get Lennox and the rest of his team. Soon SGA-1, the NEST team and Optimus where gathered.

"The three Wraiths are in the abandoned dock warehouses on the coast of Virginia," explained John, "No sighs of any Decepticons so far."

"Doesn't mean they're not there," said Lennox.

"True."

"Why there?" asked Leo.

"According to Sheppard, this area is surrounded by eighteen miles of country. They can hide there undetected by any human," answered Todd.

"Alright, we head out in five," ordered Lennox, "Optimus; bring Ironhide and Ratchet. We may need them."

Rodney and Lorne remained at the NEST complex while John, Ronan, Todd and Teyla accompanied the NEST Team. The planes landed a mile out from the dock. Following NEST standard protocol, a cover story had been created and the edge of the city evacuated, just in case this got out of hand. The three Autobots remained in their vehicle form. The dark, cloudy sky provided the perfect cover.

"We'll split up into two teams," said John, "I'll lead one and Lennox the other. Teyla will be on Lennox's team."

The Athosian women nodded.

"Ironhide, stay with Colonel Sheppard," ordered Lennox.

Sheppard and his team where accompanied by Ironhide and four other NEST solders. Lennox, Epps and Optimus took the remaining three with them. Lennox took the south side of the dock while John searched the North.

* * *

Optimus rolled quietly between the buildings. He stopped when he met up with the seven humans. He would continue when they got a certain distance ahead of him. He was scanning every building that was passed.

Teyla, Epps and Lennox reached buildings on the left while the other four searched the right. They never ventured to far into any building because of how dark they where.

"Why did Sheppard send you with us?" asked Epps.

"I can sense Wraith," answered Teyla, "I also have experience fighting them. You do not."

"She's right," whispered Lennox.

"Sir, we've found nothing," reported a young soldier.

After each row of buildings, the other four, as per orders, reported what they had found.

"Where's Jamie?" asked Lennox.

The soldier looked behind him to only see two with him.

"I don't know sir, he was just with us."

It was then that the blood-curtailing scream shattered the silence.

* * *

Ironhide followed the same pattern that Optimus had. John and Todd handled the left while Ronan and the three NEST soldiers handled the right. John had ordered Ronan to stay with them no matter what. He and Todd could handle Wraith by themselves, but those three had no experience. He wasn't going to let a single one become a snack for a Wraith.

"Sir, I've lost sight of Colonel Sheppard," whispered one of the soldiers.

"Don't worry; Sheppard can handle himself," answered Ronan.

Ronan heard it before anyone else. He knew what he had heard to. He took off running, the three confused soldiers right behind him. He heard the squealing of brakes before the black pickup was next to him.

"Get in," said Ironhide.

Ronan joined the other three in the bed of the pickup. Ironhide had detected and traced the sound. He knew where to go. He pulled around and met up with Lennox's team, who where closing on the same warehouse. Optimus and Ironhide transformed, ready for anything. The doors where ripped open. The Autobots and Nest soldiers stopped, shocked by the horrid sight that greeted them. Jamie Rodriguez, follow NEST soldier and a close friend to many, was being fed on by a Wraith.

* * *

oooo... clifhanger.

please leave me a review, pretty please?


	8. Chapter 8

Disclamor: I own nothing.

_**Flash Back**_

_t__hought_

**_Telepathic Talk_**

I also thank Botosphere for the use of their idea in the fanfiction Kinship. The idea belongs to them. I will also make some small refrences to their story and would recomend it to anyone. the story also has a segual called 'The Ties that Bind'.

Happy Easter!

* * *

Chapter 8

Lennox felt the blood leave his face. He lost all feeling in his body. He had never, in his life as a soldier, seen someone in so much pain. Time was almost frozen and Lennox watched helplessly. He couldn't save him. How can Sheppard fight these things? How many men had he watched die this way?

Neither Ronan nor Teyla could get a clear shot. Teyla felt so sorry for Lennox and his men. None of them had seen a Wraith feeding before. The first was always the worst. No matter how many she had seen, it still numbed her.

Optimus didn't know what to do. He was disgusted and sad. This Wraith was killing one of the soldiers he fought next to every single day and he couldn't help him. He knew Sam could feel his confliction emotions. He could feel Sam trying to help, but it wasn't doing any good. Ironhide felt the same as his leader. It was written all over his face.

The sound of gunfire shocked everyone back into reality. NEST solders raised their weapons, but the aging soldier was in the line of fire. More gunfire followed this time with blue-colored energy discharges. The Wraith jerked forwards and sneered. He released the man, who fell to the floor, dead. Ronan opened fire. Shots from behind propelled the Wraith forward, but he jerked back when Ronan fired and collapsed lifelessly. John was seen standing near the back of the warehouse with Todd.

"Teyla, Ronan, you two all right?"

"Yes, John," answered Teyla.

"Everyone else?"

"As well as they can be."

"How can we be alright?" demanded Lennox, "How can anyone be alright after seeing that? One of my men is dead! My man just died, screaming. How can you be so damn calm?"

"I am sorry about what happened, but you and your men where warned about the Wraith," answered John.

Lennox growled, and in his frustration grabbed the front of the Colonel's uniform and slammed him against the wall. He heard a hiss and a growl. Both Ronan and Todd aimed their weapons at the angry Major's back.

"Release him," ordered Todd.

Lennox paid the two no attention and went to return to his angry ranting, but the look in the Colonel's eyes stopped him. Lennox knew he was right when he assumed John had seen this before, but something else was there. Something that made the Major think he cared more than he was pretending. The look was haunting. It made Lennox think that every time he lost one of his men to the Wraith, he blamed himself, like he knew exactly what Jamie had gone through during his agonizing last moments of life.

Lennox let John go after the third time Todd ordered him to. He stomped out of the building.

"Are you alright, John?" asked Teyla.

"Fine."

The trip back was deathly quiet. No one spoke, no one smiled, no one laughed or made a sound. Ratchet had remained with the reserve soldiers at the planes. Optimus had sent a recording of what he had seen to the Medical Officer. Once the plane landed, the soldiers silently returned to their daily duties. The cheerful air of the base was greeted by the solemn air of the returning teams.

Sam, Mikaela, Leo, Simmons, Rodney, Lorne and Bumblebee watched as the soldier left the planes followed by the three Autobots.

"Why is everyone so depressed?" asked Leo.

"I don't…" began Rodney but finished with, "Oh no."

John, Ronan, Lennox and Epps left the plane last, carried between them was a body bag.

"Was he..?" asked Rodney when Todd and Teyla walked near them.

"Yes, Rodney," answered Teyla.

"Oh, God," chocked Rodney, "Was he the only casualty?"

"Yes," replied Teyla.

"What happened?" asked Simmons.

"Speak with your Major," answered Todd, then walked away.

Teyla nodded to them and followed the Wraith. Rodney and Lorne quickly followed the two. The remaining humans went to the Autobot hanger, escorted by Bumblebee. Optimus and the other two Autobots had already returned to the hanger.

"Optimus," called Sam as he pulled himself up the ladder and onto the table.

The tall Autobot turned to his brother as Sam made his way over.

"What happened, Optimus?" asked Sam, "I could feel that something was bothering you all the way here."

Optimus watched his brother and his human friends. The other Autobots knew something had happened, but not what; the only ones who knew where Ironhide and Ratchet and they hadn't shared with the others. They wanted to know as well as the humans, but Optimus didn't know if he could share something like that with anyone, especially someone as innocent as Sam.

Sensing his brother's fear, Sam said, "Tell me. You know as well as I that I'll ask Ironhide or Ratchet and they will tell me, even if you order them not to."

"Alright, I will show you but I warn you that you will wish you never had known," replied Optimus.

He played the recording. Sam felt sick and weak. Leo almost passed out. Simmons and Mikaela where shocked beyond words. Bumblebee didn't think he had ever seen anything so horrid in his life. What had happened was worse than anything Megatron had ever done. The other Autobots had to agree.

"That's what Uncle John has to fight every day?" whispered Sam weakly, "How can he do it? How does he stay sane?"

"Sometimes I don't think I can."

Everyone jumped. John stepped out from the shadows. Simmons hadn't known he was there. The large doors to the hanger were closed. The small human sized door on the side was hanging open. One thing everyone knew about that door was it squeaked, and made a lot of noise when opened. They should have heard him come in.

"Uncle John?"

John looked from Sam over to the tall Autobot. Optimus didn't know how long he had been there, but he felt guilty. He could feel the anger radiating of the human. He shouldn't have showed Sam; he knew that and the look that crossed John's face said the same thing.

"Why did you show him that?" demanded John rather loudly, his voice echoing in the building, "Of all the things you could have done you go and show him that?"

"Uncle John, I asked him to," protested Sam, "He did it because I asked."

"Just because you asked him to doesn't mean he had to show you a damn thing, Samuel Witwicky!"

Sam flinched. John had picked up the same habit as his parents. They used his full name when they were mad; really, really mad.

"Uncle Jo…" began Sam.

"No Sam, he is right," interrupted Optimus, "I shouldn't have shown you. You are far too young to be exposed to things such as that."

John gave them one last angry look before walking to the door. The shadows next to it shifted and the bottom of a black trench coat was seen leaving before John walked out, slamming the door behind him.

"He wasn't alone," observed Simmons.

"He's never going to forgive me," muttered Sam and he sank down to the table top.

"I do not believe it is you he is angry at," stated Optimus.

Bumblebee careful placed his hand on Sam's back before saying with his normal voice, "He cares about you and only wanted to protect you."

"I know he does, Bee, but I had to know. It wasn't Optimus' fault. If he didn't tell me I would have asked someone else."

Bumblebee continued to watch Sam sadly. He wished Optimus had never shown that to Sam, but he understood why Sam had asked. If he had known he might have told him too.

* * *

Todd followed John as he left the building. John had been there long enough to hear Sam ask how he stayed sane. Todd had guessed the human boy would ask one of the Autobots. He was close to them, particularly the yellow one and their leader. He didn't think they would actually tell him though, much less show him the holographic recording. He had told John as soon as he realized what was happening. Todd could still feel John's anger. He knew John and the boy were close and he cared about the boy greatly. He remembered how they reacted to the images as they played out like a movie to them, only they where real.

John had ran all the way from the other side of the complex, hoping to stop it before Sam saw what happened, but he was too late. He wasn't angry at his nephew. He wasn't all that angry with the Autobot, either; he could read the guilt in Optimus' face. He would have wanted to know the same thing if he was in Sam's place.

"God, I'm so stupid," muttered John, "He probably hates me now."

"I doubt it."

"How do you know?"

"He cares for you as much as you do him. He could hate you no more than you could him," replied Todd.

"What should I do?" asked John.

"Speak to him in the morning," answered Todd, "After the both of you have had time to allow the events of this day to sink in."

John and Todd shared a room. Ronan and Lorne shared one and Teyla and Rodney shared another. John collapsed on his bunk while Todd leaned against the foot of the bed in meditation. He rarely slept. He didn't need as much as a human and he never allowed himself to sleep in unknown locations. John listened to the rhythmic breathing of the Wraith until he went to sleep.

* * *

Sam felt like crap the next morning. Optimus felt guilty and he understood why. He knew he regretted showing him anything and his uncle's reaction only made the Autobot feel worse.

The air on the base was now cold and eerie; everyone knew what had happened to young Jamie Rodriguez. A plane was due to arrive today. It carried some reinforcements. Lennox didn't know anything more than that. Unfortunately he knew that IOA bastard, Galloway, was coming too.

Sam sat on a crate near the entrance to the command building. He stared at his hands. He had been sitting there most of the morning, thinking. Leo and Mikaela wisely left him alone.

"Hey, sport."

"Hello, Uncle John."

"Mind if I join you?"

"Sure, why not."

A silence followed as uncle and nephew sat there.

"I'm sorry," apologized John, "I overreacted last night. I just didn't want you to ever have to see something like that, ever."

"I know. A part of me wishes I hadn't, but a part of me is glad I did," said Sam, "There is something I need to tell you."

"Hmm…" John finally looked at Sam, showing him he had his undivided attention.

"Eight months ago, when the Fallen attacked, I was killed in Giza, by one of his Decepticons. According to Lennox, my heart stopped and I was pronounced dead."

"I read the file. Optimus was dead and you where trying to revive him with the device called the Matrix. You succeeded, I noticed."

"I did. When I found the Matrix it turned into dust. I was almost to Optimus when I died. I remember standing in some strange place and seven figures approached me; they where the Seven Primes who gave their lives to hide the Matrix. They told me that the matrix couldn't be found; only earned. After that I woke up and the Matrix became whole again. Then I revived Optimus."

John watched Sam carefully, he knew he wasn't finished.

"I spoke with Optimus after the incident and he told me that Ratchet had detected Cybertronian alloy particles in my blood. They don't produce energy, but they have been marked by a spark-energy signature. They were also not present in any of the scans he'd run before the events in Giza. He told me that I was a prime, like him. Only a prime could use the Matrix. He and I have what is called a Spark-bond, blood brothers is a good comparison for it."

John was floored. He had read the file about Giza. He also knew the big Cybertronian sun-eating machine had been approximately five miles away from where the Stargate had been found. Aliens seemed to like Giza for some reason.

"Do you member what Simmons asked me the other day?" asked John.

"Yeah, he asked how you met Todd."

"During our first year we met a race called the Genii. After a failed mission, we became enemies. A few months later a man named Acastus Kolya tried to take over the city. We defeated him. We had another encounter with him and I let him live when I should have killed him. A year later, I was captured by him on a mission. He wanted a man by the name of Laden Radim. He ordered him turned over to him or I would suffer. Weir, the expedition leader didn't turn him over on my order. I remember hearing the door open and he brought someone it. I heard Rodney shout 'he doesn't deserve this'. Next thing I knew, I was being fed on by a Wraith. After what seemed like forever, I was returned to my cell." Sam sucked in a sharp breath. "I realized the guy in the cell next to me was the Wraith. Kolya's 'sessions' continued two more times before he and I made a deal to escape together. Genii where closing in on us and I was an old man, I couldn't do anything. He feed a fourth time, leaving me barley alive. After he defeated the Genii soldiers, he came back. I told him to finish it. He told me there where things about the Wraith we do not know. He gave it back. Every ounce of my life he had taken. He called it the Gift of Life. He told me the Gift of Life was reserved for their most devout worshippers or their brothers." "That was Todd?" asked Sam. "Yeah; we are more alike than we thought," grinned John, "I understand why Optimus told you. Todd wouldn't lie to me either, but I'm still not happy about it." "I know," smiled Sam back.

"Come on kid, plane's here."

"How did you..." began Sam.

"Todd told me," grinned John, "We can talk to each other telepathically when we're close."

"That's how you knew Optimus was telling me; Todd told you."

"Yep."

* * *

Lennox watched as the plane landed. Several marines exited dressed in military uniforms. They all had the same patch as Lorne. Galloway and another man got off. The other man was dressed in a civilian uniform like Lorne with the American flag and Atlantis patch.

"Director Galloway, Mr.…" greeted Lennox.

"Woolsey."

"Mr. Woolsey."

"Woolsey? What are you doing here?" asked John as he and Sam walked up.

"Colonel Sheppard," greeted Woolsey.

"Mr. Woolsey, this is Sam Witwicky, the ambassador for the Autobots," introduced Lennox.

"Hello, Mr. Witwicky," greeted Woolsey as he shook Sam's hand.

As they headed to the main hanger, Sam could hear Galloway saying something or another about the mess Lennox had created. He stayed next to his uncle, who was talking the man who had come with Galloway.

"I'm sorry Colonel, for suddenly arriving like this," said Woolsey, "I requested to accompany Mr. Galloway when I had learned of the situation here after I had returned to earth."

"Who'd you leave in charge of Atlantis? You're here, I'm here and Lorne's here."

"Dr. Zelanka, he and Becket should be able to handle things while I'm gone," said Woolsey, "I know you have encountered the Wraith once. I also have read the data recovered on the storage device. What is your assessment of the situation?"

"We've got close to seventy Wraith hidden somewhere, an unknown amount of Decepticons and we don't know if they are working together or not, so not good."

After three hours of bureaucratic nonsense that John and Lennox hated, Galloway finally left with Woolsey.

"Bloody IOA," growled John, "They hate us, I swear."

"Galloway tried to shut us down one," said Lennox, "I threw him out of a plane."

"I heard Woolsey use to do that with the SGC, but once he got promoted to leader of Atlantis, he changed his strips."

"We need to find out their endgame. What the Wraith and Decepticon want," said Epps who had joined the two.

"Wraiths are easy, they want to get to their new feeding ground; Earth," answered John.

"The Decepticons want to rid the planet of all Humans," said Lennox.

"I think I know what they might be after," said Sam.

"You do?"

"Get everyone and meet me in the Autobot hanger," said Sam in a rush then took off.

Lennox and John looked at each other before doing what he asked. John rounded up his team while Lennox got his, which seamed to consist of too many civilians. John, Todd, Rodney, Ronan, Teyla, Lennox, Mikaela, Epps, Leo and Simmons stood on the platform with Sam as he began to explain his theory.

"The Decepticon wish to rid the Earth of all humans, this we know," explained Sam, "the Wraith want earth as a new feeding ground, this we also know; so why would they work together?"

"That's kinda the big question, dude," said Leo.

"The answer is simple. According to Uncle John, the Wraith got here in a Superhive that was powered by a ZPM. A normal hive could never reach Earth on its own. The hive ship was destroyed effectively stranding the surviving Wraith here, with no means to communicate back home," continued Sam, the supercharged cube part of his brain kicking in, "The Decepticons may be able to get a signal that far out, if so they have formed some sort of deal, giving each side what they want in exchange for cooperation. But each side wants something different for the Earth so that can't be part of the deal. Once they get what they want, they will turn on each other and fight for the Earth.

"Sounds logical," agreed Simmons, "One problem Cube-brain, if the Earth is out of the deal that what did they bargain with?"

"I don't know," admitted Sam.

"That's what we have to find out," said Optimus, "Colonel Sheppard, can you think of anything the Wraith would want besides their new feeding ground?"

"Lets see there's Atlantis, my team, m…"

"Colonel?" questioned Simmons

"I think I know what they want, and I hope to god it's not true."

"What is it Colonel?" asked Lennox, "It helps if we knew too."

"They want me," growled John, "I'm so stupid; why didn't I see it before!"

"No offence Colonel, but why you?" asked Simmons.

"To the Wraith, Sheppard is the leader of the Lanteans, the enemy. He is the one who has stopped every attempt at reaching Earth and personally responsible for killing many," said Todd.

"But not you," pointed out Leo.

"The Wraith are in the middle of a civil war. Only a certain number are awake at any given time while the rest remain in hibernation," explained Todd, "but now all Wraith are awake and are fighting over feeding grounds. My alliance with the Lanteans is for the survival of my brethren."

"Whoa, back up," said Simmons, "If some of the Wraith are suppose to be asleep or whatever then how did they wake up?"

Sam noticed how his uncle avoided eye contact with anyone. He knew something and Optimus, who had noticed too, agreed.

"It would appear as though there is something you haven't told us, Colonel Sheppard," observed Optimus.

"When we found the city, it had been underwater. The shield was failing and we couldn't dial back to Earth. We dialed to another planet, Athos, The home of Teyla's people, trying to find a place to go. While we where there the village was attacked and some of our men and Teyla's people were taken." sighed Sheppard, "The fail safe activated on the city and it rose to the surface, so we mounted a rescue. Colonel Summner, the military commander at the time, had been among those captured. When I found him he was being fed on. I shot him, killing him instantly, and then I killed the Queen. As she was dying she said she was the keeper of those who slept and when she died the entire Wraith population would wake up."

Silence followed John's explanation.

"I have a question." said Rodney finally breaking the silence, "We know what the Wraith could want so what about the Decepticons?"

"Uh… well… they want…" stuttered Sam.

"Hey, Rodney," interrupted John, "Can you contact the Odyssey and see if they can scan for unusual spikes in energy?"

"Yeah, but…" began Rodney who pointed to Sam.

"Just do it," ordered John.

"I agree, the sooner we start looking something the sooner we'll find them," added Lennox.

"Fine," huffed the scientist and he left to contact the Odyssey.

Ronan and Teyla followed the scientist and Sam mouthed a Thank You to his uncle. John left to go see what Emerson had to say with Todd following.

"Hey, kid," called Lennox, "what was that about?"

"What was what about?" asked Sam.

"That."

Sam was still confused so Mikaela clarified, "What your uncle just did."

"You told him," said Optimus before Sam could answer.

"You told him?" asked Lennox in shock, "you told him that?"

"Yes, I did. I can't lie to him anymore. He's my uncle."

"I hope you don't regret it, dude," added Leo.

"I don't," smiled Sam, "I'm glad I did."

"I am pleased you and your uncle have made up, Sam," said Optimus and the other Autobots agreed. They didn't like it when their human Prime was upset. He was one of them.

"So am I, Optimus."

* * *

Please leave me a review, pretty please?

Here is a littel something that may make you hate me.

**Preview for next Chapter:**

"Sam, I'm sorry."

"What happened Optimus? Where's Uncle John?"

"He was has been captured," replied Optimus sadly.


	9. Chapter 9

Disclamor: I own nothing.

_**Flash Back**_

_t__hought_

**_Telepathic Talk_**

I also thank Botosphere for the use of their idea in the fanfiction Kinship. The idea belongs to them. I will also make some small refrences to their story and would recomend it to anyone. the story also has a segual called 'The Ties that Bind'.

* * *

Chapter 9:

"What do you want us to look for, Colonel?" asked Emerson.

"Anything Wraith; we think they might try to contact Pegasus," explained John, "Deceptions or not it takes a lot of energy to get messages out that far."

"We'll see what the scanners pick up, but I can't promise anything."

NEST hadn't been told about the Odyssey or any other ship they had. It was a base, according to what they had been told. They had kept the location of SGC secret as well. It was unknown how the Autobots would react to that information and they needed it on a need-to-know basis.

"I hope we can finish this soon," said Teyla wishfully.

"Miss Toren?" asked John.

"Yes."

"I wanna go back to killing Wraith," grumbled Ronan.

"Of course you do," grinned John.

"Question," said Rodney, "Why did you not let Witwicky answer the question? We kind of need to know that information."

"You know the answer," stated the ever wise Teyla.

"I do," John admits, "But he wasn't comfortable sharing and it's not mine to tell. He's too young to be worrying about this."

"He's the ambassador for giant alien robots," said Rodney, "He's not exactly normal."

"He hasn't even finished collage, Rodney."

"We don't need to know, John. We will only ask if it should prove important," said Teyla.

"But…"

"Thank you."

Todd looked at John, but soon returned to his ever continuing staring contest with the Runner.

* * *

"You want this human?"

"Yes. He is very valuable to us. He also has close ties with certain individuals that will get you what you want."

"This one human will bring me the boy?"

"His capture will."

"Very well; we will capture this human for you and then complete the rest of our bargain."

"Agreed."

* * *

"Is it wise to trust these beings, Master?"

"Once I have the boy and the knowledge he possesses, neither these Wraiths nor can Prime stop us."

"How will we capture him?"

"He has been seen accompanying Prime and those humans on missions. Signal Barricade and Breakdown to prepare the trap. You will capture this Colonel, Starscream."

"Yes, Master."

* * *

"We've got two Decepticon hiding here in North Virginia Junk Yard," said Lennox.

When they had picked up the Decepticon activity, Lennox was glad for an enemy he knew how to fight. He knew that they probably wanted the information from the All Spark A.K.A Sam. That was some valuable information that could be used for god knows what.

"Todd, stay with Rodney," whispered John.

"What do you want to do, Colonel?" asked Lennox

"Your call," answered John, "You'll know what to expect.

"Alright; we will enter here, here, and here," explained Lennox, "Optimus, Ironhide and the Twins will be joining us."

Lennox explained the plan and the team set off.

"What is it?" asked Bumblebee was he and Sam watched the planes take off.

"I've got a really bad feeling, Bee."

* * *

John found the Twins amusing. He and Ronan had switched out their customary weapons for the guns used by NEST. Ronan wanted his blaster. The assault group was far larger than the last, each with saber rounds. John sent Teyla with Team Three and the Twins. Ronan went with Epps and Team Two. Ironhide rumbled along the gravel dirt as he took the second team into position. John stayed with Lennox and Team One. Optimus was crouched behind the human group waiting for the signal from his fellow Autobots.

"They are in position," said Optimus using Lennox's radio.

"Move in," ordered the Major.

Each team began closing in on the center. Both Decepticon switched forms. Breakdown charged Optimus while Ironhide battled Barricade. The Twins and humans were providing support. John had a bad feeling. He had had it since they had entered the junk yard. John blamed the junk yard. He felt like he was being watched. He turned behind him and jumped when he saw two red dots looking back. He raised his gun, but a large metal hand closed around him before he could fire.

The other two broke off almost instantly. Optimus watched as red taillights vanished into the early morning. Something wasn't right about this and Optimus had what the humans would call a sinking feeling. A loud ruckus followed by jet engines was heard.

"Starscream," growled Ironhide.

"What's he doing here?" asked Lennox.

"I do not know," answered Optimus.

"I think I do," said Epps as he came from the direction of where Starscream had been hiding, "I found this. It's Sheppard's.

* * *

His bad feeling was worse than ever. Sam paced; Mikaela and Leo watched. Ratchet had asked if there was anything he needed, but Sam didn't even know what was bothering him. Bumblebee came flying in to the hanger, faster than he should have been allowed.

"They're back," he announced as he opened the doors.

The three humans practically jumped off the table before almost diving into the car. Bumblebee left with almost the same speed. The planes landed and Optimus approached the waiting trio.

"Sam, I'm sorry."

"What happened, Optimus? Where's Uncle John?"

"He has been captured," replied Optimus sadly.

Sam felt numb for the second time since this had begun. First the Wraith feeding and now this; they had taken his uncle.

"Oh, Sam," whispered Mikaela as she wrapped her arms around him.

Sam took off running, jerking out of her grasp. She was stunned, and Leo hollered after him. He heard his friend but paid no attention. Sam knew where he was going. He threw the door open, barley slowing down. He ran down the hall, stopping at the door. He was surprised when the handle was pulled from his reach. Yellow cat eyes stared back at the panting boy.

"I know… Uncle John… told… me… you…" heaved Sam between breaths.

"I cannot."

"What?" asked a momentarily confused Sam.

"I cannot locate him. He is being hidden from me. My fellow Wraith, the ones that wish to capture him, would know that I would attempt to locate him."

"But…"

"I am sorry," said Todd as he left the room, closing the door behind him.

Todd had tried, three times, to locate John. This time he could tell that he was being blocked intentionally. The Colonel's subspace tracker was no doubt already removed. Todd glanced back at the boy, Sam. He was something precious to his brother. Todd almost left him there, but something told him he should inform the boy. The other no doubt wanted to keep it a secret to protect him.

"Come," said Todd, "Your Major Lennox has called a meeting to plan how we will attempt to find Sheppard."

Sam looked at the Wraith before following him out. After what he had seen, he was surprised he didn't fear Todd. Most of the base avoided the Wraith after what had happened to Jamie. Todd kept a brisk pace; one Sam had to almost jog to keep up with.

"I am surprised you did not go to the Autobots leader."

"Optimus was the one who told me. He wouldn't have been able to locate Uncle John."

"It is not your fault," stated Todd.

"Yes, it is," argued Sam, "The Decepticon wants me. They want the knowledge of the All Spark. They took Uncle John because they figured out they could use him to get to me."

"Sheppard would have preferred it this way. He does not want you harmed. He will never tell them what they want to know."

"But they might kill him!"

"Yes, he is aware of that."

"I can't let him die for me, I just can't."

Todd watched Sam as he tightened his hand in fists. They were so much alike. Neither was related to other by blood and yet he found himself staring at a younger Sheppard. He would do everything to save his uncle, even hand himself over.

"Perhaps…" began Todd as he stopped walking.

"Perhaps what?" asked a confused Sam.

"Perhaps there is a way for you to help him, but I am reluctant so even suggest it because many people will be angered."

"What is it?" asked Sam, "I have to help him."

* * *

Despite Todd's absence, they began discussing plans. Rodney had already had a private conversation with Emerson and found that they couldn't locate him with the tracker; that had been expected, but they tried anyway. Lorne had been beamed back to the Odyssey to see what he could do to help find his commanding officer.

"I know John wanted to keep it a secret, but it go him kidnapped," began Rodney, "we need to know what they want."

"They want…" tried Lennox trying to find some way out.

"The Decepticon wish to capture Sam," answered Optimus.

"Witwicky?" frowned Rodney, "Why?"

"You know about Mission City, right?" asked Epps.

"Yeah, read the report," answered Rodney.

"The knowledge of the All Spark was thought destroyed, but we learned that it couldn't be," explained Simmons, "All that knowledge was transferred into Sam's mind."

"Basically, Sam's head is full of alien info and Megatron wants it," summed up Lennox.

The ancient repository flashed into Rodney's mind. Maybe that was what the All Spark was some form Cybertronian repository. O'Neill had almost died the two times he had encountered the Ancient ones, so why wasn't it killing him? Rodney almost voiced the thought then the sound of rubber on pavement echoed across the building as the Yellow and black colors of Bumblebee flashed across the floor. The Autobot transformed, he looked almost scared.

"I can't find Sam," said Bumblebee.

Optimus turned to regard the smaller Autobot. He hadn't sensed that Sam was in distress or trouble and it took him a moment to realize he didn't sense him on base.

"If that Wraith…" warned Lennox, thinking the lack of Wraith meant something.

"He wouldn't," shot Rodney, but turned to his fellow team mates concerned, "Would he?"

"No, Rodney. I do not believe he would hurt Sam," answered Teyla.

"I'm going to kill him," growled Ronan.

"This may not be related at all," Suggested Epps, "First we need to figure out if they are both on base."

"Sam is not," said Optimus.

"I can not sense any Wraith presence," answered Teyla.

"I'm definitely going to kill him," Ronan growled again.

* * *

Sam was confused. He had been confused a lot lately. He began to wonder if this was normal for his uncle. He heard the scientist named Lee chattering in the background with a woman named Samantha Carter. They where talking with Todd.

When he had first arrived, they were 'beamed' into the briefing room, as Todd called it. He could see the Stargate, as it was later explained, from that room. General Laundry, the man he met when he first arrived, had not been happy at all. After the five minute rant, which Sam heard behind the closed door of his office, he had been given a visitors' pass and told not to wonder around.

"Will it work?" asked Lee.

"I do not know, Doctor, but this may remain our only hope."

"Don't you think you acted rashly?" asked Carter, "I mean you practically kidnapped the boy. This will not look good to the NEST higher ups. General Laundry is calling General O'Neill, but we're still going to have a lot of unhappy people."

"We are running out of time, Colonel Carter. Neither I nor the Odyssey can locate him, we don't know where to begin looking, and your planet is simply too large to scan for Wraith life signs."

"But we don't even know if he has the gene; this could be a waste of time," argued Carter.

That caught Sam's attention. He remembered what Ratchet had said about his uncle when he found the strange DNA he had.

"Um… excuse me?" The three turned to look at Sam. "You said there was some why to find him, how?"

Carter picked up the device and pushed it in front of Sam. It looked like a box with a keyboard sticking out with odd letters on it.

"This device was found last year on a mission led by Colonel Sheppard; its function is finding hidden things." explained Carter, dummying it down best she could, "We have used it to locate two underground outposts that we otherwise would not have known where there. The device needs a certain gene to be activated. With luck you have this gene and can use it to locate Colonel Sheppard, but the percent of people with it are very low."

".00005%," recited Sam from memory, then added, "Ratchet told me," when he received confused looks from Carter and Lee. This further confused Lee, who hadn't the NEST briefing.

Sam slowly reached for the device, hoping he was one of that .0005%. He had to find his uncle, even if it killed him.

* * *

Please leave me a review, pretty please?

If i start turning characters OOC please tell me, i'm not a fan of OOC.


	10. Chapter 10

Here is the long awaited chapter ten. I shall hopefuly have this all wraped up in the next one or two chapters. There is something a the bottom that i would like you all to look at but i don't want to keep you waiting anymore so enjoy!

_**Flash Back**_

_t__hought_

Telepathic Talk

I also thank Botosphere for the use of their idea in the fanfiction Kinship. The idea belongs to them. I will also make some small refrences to their story and would recomend it to anyone. the story also has a segual called 'The Ties that Bind'.

* * *

Chapter Ten:

The ground was damp. The smell of rotting wood and mold attacked his senses. John tried to push himself up but pain shot through his tired arms. John began to notice his surroundings. Crates and fallen beams covered the ground. He slowly drug himself to the edge of the catwalk he was on. He estimated he was about fifty feet from the ground, to high to jump. Both ends of the catwalk were broken, he was trapped up there. Growling, John shoved himself up. Once he had his balance; he noticed that one side of the catwalk had a ladder at the end. The gap between the two pieces was about twenty-five feet.

His team would be looking for him, he knew that. Sam would want to help, the two of them where too alike. That fact had proven a blessing and a problem for years. Of course, Sam wanting to find him would mean Optimus and the other Autobots would be looking as well.

Returning to the matter at hand, John knew he'd have to jump. He had also guessed that the Odyssey wouldn't be able to find him. The pain in his arm only confirmed what he knew. After flexing his legs to get the blood moving, John took a running leap. He barely made the jump. Landing on the other side, he rolled to his feet before starting to climb down the ladder.

Someone put him up there. His guess was someone big. He remembered the hidden Decepticon grabbing him and then blacking out. Somehow he had to let them know where he was but he was no McKay or MacGyver for that matter. He jumped the last few steps. Landing he found a small door on the side. He opened the old, creaking thing a quietly has he could. The door led to another part of the old building. He kept to the shadows as walked along the wall. Being friends with Todd had helped him figure out how the Wraith managed to lurk so well. Part of it had to do with just being a Wraith but the other part was skill, one John was beginning to pick up. He froze when he heard voices.

"We have the human, now you will tell me how he will bring me the human boy," demanded a loud voice.

"The boy will be delivered as promised," answered a voice that was defiantly Wraith.

Peeking out from his hiding place, John saw what had to be a Decepticon. He felt his stomach drop. This had to be Megatron; he looked exactly how he had been described. The Wraith was standing on another catwalk, almost level with the Decepticon's face. John didn't recognize him but it was dark. As John began moving again he bumped a crate causing the metal pipes lying atop it to fall off. Megatron wheeled around and began scanning the area. John cursed himself and ran. He ran as fast as his legs could carry him. He heard the defining shouts of the angered Decepticon and knew he would never outrun him.

* * *

Sam heard voices, not the ones he normally heard either. The device in front of him sprung to life as he touched it. A map appeared in what was a holographic display. It showed the Earth, rotating as it would in space before zooming closer. First the United States appeared bigger and it closed in on one state, then a city, then an area.

"Well?" asked Carter.

"The place you call Virginia," answered Todd, "The same place we first encountered the Wraith."

Sam removed his hand as quickly as he could and the voices when away. The device shut down.

"What now?" asked Sam.

"I will signal the Odyssey and a team will be beamed to that location," said Carter, "Todd, you will be beamed there as well and I'll have the Odyssey send Mr. Witwicky back to Diego Garcia."

"No!" protested Sam, "I want to go!"

"You aren't military trained; I can't send you into a potentially dangerous situation," said Carter.

"I've survived the attack on mission city and what happened in Giza," pointed out Sam, "I can handle myself against Decepticons!"

"That's not the point!"

"Colonel Carter, I do not believe you will change his mind."

"Todd, you cannot possibly be considering…"

"I have to go," interrupted Sam, "I have to. If I don't, I may never see my uncle again. I am the only one who can save him."

"Colonel Sheppard has been fighting for his life against Wraith for six years; he knows how to take care of himself."

"Colonel Carter," began Sam, "These Decepticons want me, and they will kill him if I don't go."

"All the more reason for you to not go, John will sacrifice his life if it means he could keep you safe," replied Carter, "He would never forgive himself if something happened to you."

"And I won't forgive myself if something happens to him."

* * *

"Why the hell did he take him there!" demanded Rodney in his ear piece.

The NEST team and four Autobots watched as the scientist yelled at the unseen person on the other end. Ratchet and Ironhide had both entered the building when Sam was discovered missing. To call any of the Autobots happy about the situation would be like trying to call lava cold. Oh, if looks could kill. Ronan was glaring and Teyla was trying to convince Lennox that Todd had a very good reason for kidnapping Sam.

"That Wraith is not going to live long after this," whispered Epps.

Mikaela nodded her agreement. Wraith or not, no one kidnaps her boyfriend.

Rodney could not believe how stupid Todd had been. He kidnaps the Witwicky kid and then takes him to the SGC; for what reason? This kid's car was an alien robot and the others seemed pretty attached to him too, if they didn't kill Todd, John would. He listened to the other man before demanding to talk to someone with a little more intelligence and someone who could explain exactly what was going on. That's when he was redirected to the SGC and Carter.

"_Sorry about this Rodney," said Carter, "We have had an interesting development here."_

"I know," barked Rodney, "I need to talk to Todd and see what going on in that twisted Wraith brain of his."

"_He's not here right now, neither is Sam Witwicky."_

"What the hell do you mean he's not there anymore!" demanded Rodney.

Lennox and Optimus looked straight at the scientist at this point causing him to fidget under their gaze.

"_Rodney, I need you to hook up your radio so that everyone will hear this.  
_

Confused but compliant, the scientist did what he was asked. He hooked up the radio to one of the computers.

"_Major Lennox, I am here with General O'Neill and he has orders for you, your team and SGA-1," said Carter._

"Fine; then let's hear them," growled Lennox, still very unhappy.

"_Prepare to move out," said O'Neill, "We have the coordinates we need."_

"For what?" asked _Simmons_.

"_The rescue of Lt. Colonel John Sheppard."_

* * *

Sam was in awe. They had a spaceship! He and Todd had been beamed directly to the Odyssey before they were to be beamed to the coordinates. Lorne and a number of marines from Atlantis who had been sent back were to join them. Lorne was as unhappy as Carter when he learned that Sam was going with them.

"He is a civilian." stated Lorne slowly, like he was talking to a child, pronouncing each word shapely.

Todd gave the major a nonchalant stare. "I am not going to have this argument with you Major Lorne; the boy is coming with us."

Sam was staring out the window, at Earth. This is what it must have looked like to the Autobots when they first came here. He felt bad that he didn't tell anyone where he was going but if he had, someone would have stopped him. Everything was his fault. If he had stopped them from leaving then his uncle wouldn't have been abducted by Starscream. Sam turned when he heard someone clear their through behind him.

"Alright kid," sighed Lorne, "You're not military, but I expect you listen to me. I call the shots on this mission."

"Yes, Sir."

"I can believe I agreed to this," said Lorne to himself, "you will stay with Todd or me and do not wonder off."

Sam nodded again with a "yes, Sir."

"Good, now follow me."

* * *

Pain racked his body. He couldn't move, couldn't scream, couldn't do anything, at least not anymore. John had thought it would have been bad if the Decepticon got a hold of him but the sneering Wraith had been worse. He didn't take much but it still hurt. He swore to himself that he would never become Wraith chow again but here he was getting fed on by a Wraith. John guesses it was only five or ten years but still…

"Now Colonel Sheppard, are you willing to tell me what I want to know?" asked the Wraith.

"Todd is going to kill you."

"Ah yes, the former commander still lives then. I was wondering if you had killed him after our last encounter."

"He'll kill you for betraying him," said John again as he felt darkness creeping up.

"Maybe," said the Wraith, "but, he will bring us the boy."

"Todd would never hand Sam over to you," growled John.

"Oh yes he will, in fact he is already here with him."

"No!" growled John again before he lost consciousness.

* * *

They had beamed down in a circle with Todd, Lorne and Sam in the middle. Before they left, Todd had shown Sam how to use a Stunner. He had also been given a radio and a vest. The marines spread out, but Sam stayed close to Todd and Lorne. Lorne performed a few hand signals and the marines broke into two groups of five. Todd tugged Sam with him as he headed right; Lorne went left with the other group. As they broke apart Sam saw Lorne pull out a white colored device from his vest. It took him a moment to realize Todd had a similar one, but Todd handed it to him.

"I can't use them," whispered Todd at Sam's confused look, "It is Lantean technology."

"What is it?"

"Life signs detector. The white dots represent living beings."

Sam looked down and saw seven dots clustered together. He knew it to be the marines, him and Todd.

"Signal when one is approaching our position," said Todd.

Sam nodded.

* * *

They had been beamed to the other side of the location, courtesy of the Odyssey. Lennox was mad about Sam, now he was mad that they were never told that they had a ship, let alone four. Those things would have been helpful against the Decepticons. Optimus had been mildly shocked but mostly surprised that the United States government had kept the ships hidden from the Autobots. When he had questioned Rodney about it the scientist had told him that they were probably not in orbit when he had originally landed.

Teyla watched Lennox as he stood next to the Peterdilt diesel engine; she was surprised when he hadn't taken all the Autobots with them. She knew every single one of them was ready to go and rescue Sam. Sideswipe, Arcee and Jolt were left back at base. Lennox had looked like he was going to leave Bumblebee with them, but after the yellow Autobot said he would swim all the way here, despite any order given to him by Optimus, he had to bring him. Lennox had brought the Twins, Ratchet and Ironhide as well.

"Alright, listen up," said Lennox, "Lorne has his men coming from the east. We'll fan out and meet his team half-way. I don't... I don't want a repeat of last time so no one and I repeat no one goes into anywhere without back up. Stay in radio contact at all times."

With a swift nod from the solders, they set out. Rodney pulled out the life signs detector he always carried with him. He let out a breath when he saw that it could pick up an Autobot, even thought the dot was twice the size of the ones for humans. The Auto bots had taken position in between their human companions, allowing them to fan out more.

Optimus made sure to keep track of everyone who had come with them. He never let anyone get too far ahead of him. He knew the other Autobots were doing the same. He had called out to Sam as soon as they had arrived. Sam didn't answer. Optimus couldn't tell if Sam had even heard him or not, he couldn't even tell where his human brother was and that left the Autobot leader terrified.

* * *

"Ah...Todd?" called Sam quietly.

"Hmm..."

"This thing show several people in that warehouse."

Todd looked over Sam's solder at the detector. It had twelve small dots and three large dots.

"I'm also sensing Decepticons," added Sam.

"I can only assume the Decepticons are the ones reading as the larger life form," said Todd, "Then the other reading are Wraith."

"Are you sure it's not Lennox and his men?"

"Yes, we Wraith can scene the presence of other Wraith; just as you can tell when there are Decepticon near; so can I with Wraith."

"But can't they tell that you are near?"

"Normally yes, but I am far older than many of my species," chuckled Todd, "and have proven more than capable of hiding myself from them."

"Is Uncle John in there?"

"I do not know, but that is most likely the case."

Todd called one of the Marines to him, a captain by the name of Benadickt. He told the Captain that he was to take the rest to the front while he and Sam would come around the back and on his signal cause a distraction that would allow them to sneaking unnoticed.

The marines moved to the front and opened fire on the warehouse door, the bolts easily pierced the aluminum door. Shouts and orders could be hears from inside, the loudest being in cybertronian. Sam recognized the voice as Megatron. He knew instantly that his uncle was near.

* * *

The aluminum building echoed the gunshots. Lennox broke out into a run with Epps and Ronan right behind him. As they neared the warehouse Lennox saw Lorne coming from the opposite direction. His blood ran cold when he didn't see Sam. He was about to demand to know where the kid was but Decepticons coming though the warehouse next to them stopped any word that were going to leave his mouth.

The rear entrance of the building was easy to find. Sam slipped in right after Todd. He could barely see into the black abyss. He could hear the fighting outside but none of it mattered, he had it find hi uncle. Todd pointed to an old door; Sam nodded. He pulled the door open, slowly. Todd stood behind him, watching the area. Sam pulled the old, rusted door open. He slipped in without a sound, Todd followed.

* * *

Rodney didn't know where they had come from, but like Wraith, there seemed to be an endless supply of them. They'd kill one Decepticon and another would take its place. Rodney decided he liked Wraith better. Sure they could suck out your very life-force, in a space vampire kind of way, but at least they didn't tower a hundred stories above your head. Benadickt had informed him that Todd and the Witwicky kid had snuck around back to find John. Lennox, Optimus, Lorne and he had not been too happy to find out about that. He just hoped that nothing bad happened but he knew it would, it always did.

* * *

Sam could see someone sitting near the far wall.

"Uncle John?" he called softly.

He got no response. He felt a tap on his solder and looked over too see Todd held out a flashlight to him. He couldn't help but wonder if there wasn't anything Todd didn't have hidden on him. Sam took the flashlight and turned it on. When no immediate attack came he shinned it around. It finally landed on the person sitting in the corner.

Sam wished he hadn't had the flashlight now. The sight that greeted his was worse than the recording he had seen of Jamie. Never in his life had he wished he could unseen something. It was his uncle and he was alive, but he wasn't supposed to look like he did. He wasn't supposed to look helpless, weak, old.

* * *

**Please Read!**

Sequel to Transformers: The Atlantis Factor.

Alright everyone, I know a lot of people have enjoyed this story and I've got a chapter, maybe two left to go so I want feedback on this soon. I have a poll on my profile that I would like you to vote in and I have a few questions to ask you that I would like answered in a review or PM along with your opinion on the story of course.

1) Should I write a sequel?

That's actually all I need to know. It will take place after Transformers: Dark side of the moon so it could contain spoilers. It's an awesome movie, by the way, and I recommend it to anyone. I've actual kind of have a plot forming in my had already so if you want to know what it is let me know and if enough people do I will tell you at the end of the next chapter but until them my dear fans please read and review!


	11. Chapter 11

Here is a early Thansgiving gift and a leate halloween present. Chapter 11. Enjoy!

_**Flash Back**_

_t__hought_

Telepathic Talk

I also thank Botosphere for the use of their idea in the fanfiction Kinship. The idea belongs to them. I will also make some small refrences to their story and would recomend it to anyone. the story also has a segual called 'The Ties that Bind'.

* * *

Chapter 11:

Sam was flooded with emotion, some he couldn't even begin to decipher. He felt lost and confused. Nothing made scene anymore; his world was slowly falling apart at the seams. He felt he was losing his last ounce of sanity. His mind screamed for everything to make sense, he wanted things to be simple again. His emotions didn't let his mind register the flashlight falling from his grasp or it hitting the ground. He knew his uncle was still alive, some small part of his mind recognized that as his chest slowly rose and fell. Todd was kneeling next to him, muttering something inaudibly.

Sam knew Jamie's death had been painful but he had died. This was far closer to home. The full gravity of what his uncle had been dealing with had finally hit him. Sure, he knew about how he and Todd had met, what had happened but somehow it hadn't hit him all that hard, until now. He couldn't imagine his uncle like this, and seeing it only brought reality upon him all the harder.

John Sheppard was invincible; Sam had believed that all his life, his invincible uncle who fought the monsters in his closet, the ones under his bed. Nothing could defeat him. Now Sam saw the terrifying truth that was bringing his world down around him. His uncle wasn't invincible, he could be defeated, and he was human just like the rest of them. Never in his life had Sam felt so terrified, not when he faced Megatron in Mission city or the Fallen in Giza. Sam felt everything crumbling around him, leaving him helpless.

* * *

Optimus felt a sudden flash of emotion. Fear, confusion, and helplessness all vibrated through his spark. His fear for Sam increased tenfold.

The Decepticons were endless and the wraith drones fired from the roof. The Wraith stunners did not affect them to the extent it did the humans because of their protective armor a well placed shot could paralyze them. Ironhide was short an arm because of a stun blast that had hit his shoulder and caused his circuits to go offline.

Ronan assured Lennox that it would wear off but Ratchet wasn't sure. He knew everything there was about repairing the others but he knew next to nothing about these stunners. According to the information from Todd, the stunners affected a human's nervous system. They disrupted the messages from the brain and caused them too temporarily shut down But Todd had confessed that he did not know how this would affect the Autobots. Which caused a whole another problem for the medic because he was the one who would have to repair them.

"Major, I must get to Sam," stated Optimus barely keeping his desperation out of his voice.

Lennox risked a quick glance at the Autobot leader and only through his years of knowing Optimus did he see the desperation he was trying to hide.

"We'll hold them off best we can," answered Lennox, "go!"

Ronan and Lorne nodded to his statement before braking off and shooting at the Wraith on the building.

Ironhide and Ratchet quickly moved to clear a path for Optimus. Within a matter of seconds they had created an opening between the enemy ranks. Optimus jumped toward the gap and transformed into his alternate form mid dive. He landed and floored the peddle, speeding around the building.

Ronan and Lorne let a team behind the Decepticons and began taking out the Wraith. Lennox and his men kept the Decepticons off of them as they fired.

* * *

Without warning Todd stood and grabbed Sam by the back of the tact vest and shoved him behind the door, He then pushed the unconscious colonel into him.

"Stay here," ordered Todd, "do not move from here no matter what happens."

Sam numbly nodded before Todd disappeared through the door. Sam didn't like how light his uncle felt. Sam felt a calmness rushing his way and knew it was Optimus. They others had arrived. Sam felt better knowing that the Autobots and Lennox was here. He heard a loud crash and felt he should investigate but stayed as Todd had ordered. The first crash was followed by another and another before what sounded like stunners being fired. Sam pulled the stunner he had been given and held it near him, ready to fire if he had too. The sounds of fighting stopped and he froze when he heard someone approaching the room. A thousand questions burned through his mind at once. Was it Todd? Did he win? What if he lost? Who was coming? A shadow passed the door and Sam reacted and pulled the trigger. A sudden jerking motion caused the shot to turn left as the stunner was yanked sideways.

"I admire your reflexes but…" said Todd leaving the sentence open.

Sam blushed in embarrassment, "sorry."

Todd shook his head, "I should have warned you before approaching."

Todd moved John so he was lying on the floor. He looked up to say something to Sam but the sudden sound of metal straining before giving way interrupted him. A large, clawed hand shot through the wall behind Sam and enclosed around the boy before pulling him backwards.

* * *

Optimus felt relieved when Sam responded by send happiness back to him. It felt good to know his brother was alright, for now. He sped up. He didn't know how long Sam would remain safe. He Optimus rounded the back of the building and found the door Sam had used to enter. This warehouse was like all the others which meant that there would be another entrance on the left side. He quickly headed toward it but as he heard he felt Sam's sudden and silent scream for help.

* * *

Sam screamed for Optimus with all the emotions he could muster. He knew he was close but it still might not be close enough.

"Thought I'd forgotten about you boy?"

Sam stared back at the red eyes of the Decepticon leader. He didn't trust his voice to not betray his fear. It took every fiber of his being to not completely panic.

"_Oh__God,__please__hurry__Optimus,__"_ prayed Sam.

"So this is the boy you so desperately wanted," chuckled a very wraith-ish voice.

Megatron turned to look at the grinning creature standing behind his shoulder.

"I believe we can now conclude our deal."

"Yes, I believe we should," replied Megatron.

Megatron turned toward the Wraith. Sam had a feeling he knew what was going to happen next. Megatron raised his other arm and fired. The Wraith was disintegrated as shock appeared on his face.

"Such useless creature," commented Megatron idly before looking back at Sam.

Sam felt a shudder go though his body. He didn't know if Megatron was going to kill him. What would Optimus say to his parents if anything happened to him? What would Uncle John say? Sam felt the grip around him become more constricting. Megatron opened his mouth to speak but a gunshot echoed inside the building and Sam saw the spark s from the bullet hitting Megatron's face. Both Sam and Megatron looked toward where the bullet had come from. Sam's eyes widened as he looked at the man standing across the warehouse.

"Let my nephew go!" declared Lieutenant Colonel John Sheppard with all his might.

* * *

Todd covered John as the debris fell around them. Todd cursed himself for not being aware that some Decepticons where still in the building. He knew the only remaining wraith was his traitorous second commander. He had killed and fed on those that had stayed inside the warehouse and the Runner no doubt had killed ever wraith outside.

The hole in the wall was huge and Sam was gone. Todd could only assume that it had been the one who kidnapped John or the Decepticon leader himself. Todd quickly resumed what he had intended to do. With a silent apology Todd opened the front of John's shirt and placed his feeding hand on the center of his chest. With all his will Todd forced every ounce of life he had taken and slammed it into  
John.

John felt sudden, searing pain radiate from his chest and he panicked. The wraith was back. He tried to struggle but found himself unable to. The pain slowly brought him back to consciousness. It wasn't until he was fully conscious that he realized that pain was gone. Whoever it was had stopped. Then he noticed something else that was not right. It was easier to move, his body didn't feel old and weak. He shot up as fast as he could.

"I am please that you are alright."

"Todd?" questioned john, "What the hell happened.

"I restored your taken life. Now we must hurry or your nephew may be in danger."

"You brought Sam with you?" cried John in outrage.

"He was rather persistent despite what myself and others said," replied Todd, "He is too much like you, he refused to take no as an answer."

"That still doesn't mean you had to bring him!"

"What would you have done if your positions were switched?" asked Todd.

John settle for glaring at the Wraith because he knew Todd already knew the answer to his own question.

Todd pulled John to his feet and John quickly jumped through the hole Megatron had created seconds after Todd had handed him a 45. Locating Megatron hadn't been all that difficult because the hole created a tunnel that led right to him. When John reached the other end he dropped to the floor and found a better vantage point near a large aluminum door.

"Such useless creature," commented Megatron idly after he had destroyed the wraith. The Decepticon leader turned back toward his nephew.

John could read the fear in Sam's face. He sucked in a large breath of air and fired the gun. He hit his target but it did no damage. Both looked at him and once he knew he had their attention he declared, "Let my nephew go!"

* * *

Lennox said a silent thanks to whatever deity would listen to him. The Decepticons and wraith were finally dead and no more were appearing.

"We need to get this door open," said Lorne.

"Allow me," grunted Ironhide as he aimed his cannon toward it.

Before Ironhide could fire or anyone utter a protest on the matter a gunshot echoed throughout the building; Lennox was filled with dread.

"Wait," called Lennox, "blowing down the door may not be such a good idea."

"I agree," said Ratchet and Bumblebee nodded.

Ironhide looked at his fellow Autobots before powering down his cannon. He moved out of the way as Ratchet and Bumblebee moved forward. The two pulled the door from the building. While it wasn't as silent as some would have liked it was quieter than the Weapon specialists' cannons.

"Let's go," said Ronan.

* * *

Optimus didn't stop, he didn't slowdown. Once he saw his entrance he sped toward it was fast as he could. He launched himself into the air and transformed. He dove through the door. Optimus registered one thing as he came through the door, Sam and he was in danger. Optimus collided with Megatron. In an attempt to defend himself, Megatron released his grip on Sam and Sam dropped down into Optimus' waiting hand. He wrapped his fingers around Sam to protect him as he and the Decepticon Leader rolled. Once they came out of the roll, Megatron jumped away from Optimus and growled. Optimus barely had enough time to set Sam down as Megatron tackled him, ready to fight.

Sam ran away from the two as fast as he could. A sudden grip on his arm told him someone had grabbed him. He looked up and into the face of his uncle who pulled him forward, leading him away. Now that Sam wasn't staring death in the face he realized that John was no longer old.

"Wha-Uncle John how?" stuttered Sam.

"Not now!"

John pushed Sam out the door Optimus had come thought. Todd was already waiting. Optimus and Megatron could still be heard fighting. A crash and the sound of someone being thrown was heard seconds before Optimus came sliding out the door. Before he could charge back in Megatron came out and tackled him. Optimus regained his footing quicker and kicked Megatron into the building next to them. Megatron crashed through the side and the force caused a good portion to claps on top of him. While Megatron tried to get loose form the pile Optimus fired a shot into his left shoulder. Megatron cursed in Cybertronian. Before he could retaliate shouts filled the air; Lennox and the other Autobots had arrived. Megatron cursed again and changed into his jet mode and took off.

Optimus kept his gun trained on Megatron until he was out of range.

"You alright Optimus?" asked Sam.

"Yes Sam, are you alright?"

"Yeah," grinned Sam.

"Kid," called Lennox angrily, "don't you ever do something like this ever again!"

"I must confess that I agree with Major Lennox," said Optimus.

"How about we worry about this latter," sighed John tiredly, "I for one would like to get out of here."

"I think I could agree to that," added Epps.

The Odyssey beamed the NEST team back to Diego Garcia. John was beamed to the SCG along with the marines and his team. As soon as he arrived, John was escorted to the infirmary where he could be checked over.

Sam was not happy when he was sent back with the NEST team. He had wanted to stay with his Uncle. Lennox contacted General O'Neill to see if Sam could be sent over to where John was. Optimus felt Sam's anger when the General's reply was no.

"NEST and the SGC will go back to normal operating procedure as if this never happened," said O'Neill. He cut off the video feed before Lennox could say what had crossed his mind.

"That's BS," declared Epps.

Leo, Simmons and Michaela had to agree with him. Several of the Autobots agreed too.

"I am sure your uncle is fine Sam," assured Optimus.

* * *

"Why the hell not?" demanded John, "the kid's already been here."

"The reason Mr. Witwicky being allowed on base was extenuating circumstances," explained Laundry, "The SGC and NEST were not designed to work together, and don't even get me started on the issues the two programs could cause each other."

"That still does not explain why Sam is not allowed to visit me, I'm worried abut him and we need to talk. He already knows about the SGC so is not a clearance issue. He's also the official Ambassador for the Autobots; doesn't that fit into the SGC mandate of exploring alien species?"

"The Autobots aren't so alien anymore, Colonel. They live on earth," pointed out Laundry.

"So does Teal'c."

"He's not considered alien either."

John looked at the General before turning to glare at the heart monitor, he knew he had lost. When he had returned Becket had insisted that he be monitored for a day or two. Since Keller had become the Chief Medical examiner at Atlantis and Beckett was technically dead he had been working on the different ships and sometimes at the SGC. He did make somewhat regular trips back to the city.

Since he had been on earth when John was brought in and he was the most experienced when it came to wraith feeding they had brought him in. John had insisted he was fine and Beckett believed he was but wanted to make sure so he was stuck in the infirmary.

John had already warned Todd about dragging Sam into danger again and swore he'd shoot the wraith next time he did. Todd had just chuckled, knowing his human brother would not carry out his threat but understanding why he had said it. He hadn't wanted to drag Sam into anything but the boys stubbornness and unwillingness to take no had left little choice. John knew that if Todd hadn't taken him then Sam would have found another way to get there. They both were glad that it had worked out in the end.

"This was an interesting week," said John.

"It was fun too," grinned Ronan.

"It was interesting," agreed Teyla.

"Interesting, yeah sure, now I'm behind on my work!" complained Rodney.

"I believe you will have plenty of time to catch up when we return to Atlantis, Dr. Mackay" said Todd.

"Once I get out of here I'm heading back, we kinda just took off on Ron and Judy. They're probably worried sick. I also left my truck at their house."

"I'm sure they are fine John, according to what you said they knew where you were going," assured Teyla.

"Doesn't mean they're not worried."

"Well son, if you get some sleep I'm inclined to let you out tomorrow," said Beckett as he walked up, "but that's if you get a solid night of sleep and pass all of your tests tomorrow."

"Alright Doc," grinned John.

* * *

Sam didn't know how to feel when Optimus pulled up to his parent's house. Sam wasn't sure how his parents would react when he didn't show up with Uncle John. Optimus has promised to stay and help explain best he could. Sam stepped out of the Truck and Optimus' holoform appeared next to him. With a nod from his brother Sam headed to the house. He managed to make it to the living room before his mother found him. His dad gave a nod to Optimus.

"You're alright Sammie," cried Judy happily, "I was so worried."

"I'm fine Mom, really."

"Where's John?" asked Ron when he noticed the Colonel was absent.

Sam noticed his move freeze and turned several shades of white. She looked at him with a thousand questions that she could not voice cross her face.

"He's fine mom," said Sam.

"But where is he," pressured Judy.

"He's…" began Sam but a knock at the door interrupted him.

Optimus and Ron both stepped out of the women's way as she practically ran to the door. When she opened the door she just stared. Her mouth opened and closed without saying anything.

"Hey Judy, sorry I took off before."

"You're alright," she suddenly cried. She nearly knocked him over with the force of her hug.

Sam come out when hear him mother. He was happy to see his uncle again. Him mother had just let go of him when he hugged him.

"Hey kid."

"Why did you two leave so fast," asked Ron once Sam released John.

"Looks like I've got some explaining to do, huh?" chuckled John.

"We've got some explaining to do," corrected Sam.

"Yeah, I guess we do."

* * *

please leave me a review, pretty please?

I have a pole on my profile so if you could then please answer it.


	12. Epilouge

Here is the long awaited end to my story. I will write a suqual but i need ideas so could you guys please send some of yours my way, thanks a lot.

_**Flash Back**_

_t__hought_

Telepathic Talk

I also thank Botosphere for the use of their idea in the fanfiction Kinship. The idea belongs to them. I will also make some small refrences to their story and would recomend it to anyone. the story also has a segual called 'The Ties that Bind'.

* * *

Epilogue:

The explanation had gone better than expected. Judy had wondered why she couldn't know any normal people but beyond that and the shock everything had worked out as John had planned. It had taken a day for John to get Judy and Ron cleared to know about the Stargate program, it was actually easier than it should have been because they had clearance for NEST. It also helped, as John had pointed out to General O'Neill, that Sam would tell them anyway and since he was not bound by SGC protocol they couldn't do anything about it. Even if they tried, John didn't think Homeworld Security was up to arguing with Earth's very own, several stories tall, Autobot protectors. Optimus had been a great help in explaining too, John thought the holoform thing was cool.

"Optimus is going to be joining us then?" asked John as he and Sam walked down the street.

"Of course, I'm just glad I don't have to come up with some random explanation to explain who he is."

"So am I, you're a terrible lier."

Sam pretended to look insulted before laughing. John joined in.

"Here I've got something for you." John handed Sam a box wrapped in light blue and green paper.

Looking skeptically, Sam pulled the paper off and opened the box. Inside he found a silver pendent in the shape of some funny looking symbol on a silver chain. He looked at his uncle curiously.

"It's a tracer," replied John with a grin, "that way if you want to disappear on everyone again they can find you."

"You're never going to let that go, are you?"

"Eventually, but you got off easy. Todd gets to spend the next week with Mackay," said John, "I'm not sure who's getting tortured more, him or Rodney."

Sam agreed as he slid the necklace over his head, "What's this symbol mean?"

"Oh that? It's the Wraith symbol for friend. Todd gave that to me on a mission. I had to pretend that I was a worshiper so I couldn't have my subspace transmitter or my radio. He's got the signal encrypted so the only ones who know it is him, the SGC, Atlantis, me, Optimus and I'm sure he's told NEST and the rest of the Autobots."

"Sammie, John!" called Judy from the house, "dinners ready!"

"Come on kid," ginned John as he grabbed Sam by the shoulders and ruffled his hair.

"Uncle John?"

"Yeah?"

"Next time, don't wait so long to visit and thanks for everything."

"No problem. Hey, maybe next time you could come and visit me."

"I'd like that, a lot."

* * *

please leave me a reiew, pretty please?

*sighs* one story down, half a million to go. Anyway, Thank you all for reading my story and I'd like to thank CelestialMoonDragon for beta reading this for me. I know I can be a pain in the ass but thaks sis.

* * *

**A little bit about the Sequal:**

I know who is going to be in it and that it takes place in the Pegases Galexy but other than that I really don't know at this point so please give me som of your ideas and i really need a title for it too so let me know what you think i should call it.


End file.
